Compositions and methods for production of disulfide bond containing proteins in host cells

ABSTRACT

The invention provides composition and methods for producing proteins of interest which comprise at least one disulfide bond, include proteins which in their mature form do not contain disulfide bonds, but whose precursor molecule contained at least one disulfide bond. The methods employ a host cell modified to more efficiently produce properly folded disulfide bond containing proteins. The host cells generally contain a mutation in one or more reductase genes, and can be further genetically modified to increase their growth rate, and are further optionally modified to increase the expression of a catalyst of disulfide bond formation. Host cells, methods for using such to produce proteins of interest, proteins of interest produced by these methods are within the scope of the invention.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.09/679,705, filed on Oct. 5, 2000 now U.S. Pat. No. 6,872,563; whichclaims the benefit of priority to U.S. Provisional Application No.60/157,770, filed Oct. 5, 1999; U.S. Provisional Application No.60/163,939, filed Nov. 8, 1999; and U.S. Provisional Application No.60/166,044, filed Nov. 17, 1999, the contents of which are specificallyincorporated herein.

STATEMENT OF RIGHTS

This invention was made during the course of work supported by NIH 5RO1GM55090-02. Thus, the U.S. Government has certain rights in theinvention.

BACKGROUND OF THE INVENTION

Overexpression of many secreted proteins which are stabilized bydisulfide bonds cannot be obtained by mere expression in bacterial hostcells, due at least to the reducing cytoplasm of E. coli. Such proteinseither become degraded or are found insoluble in so-called inclusionbodies. This problem is often addressed by alternative expressionstrategies such as export of the protein to the periplasm of E. coli orexpression in another organism. These strategies are laborious,requiring the recloning of genes of interest in other vectors. Inaddition, certain proteins of particular interest, e.g., pharmacologicalinterest, cannot currently be produced at high levels an in active formin bacteria.

The following is a summary of the current knowledge in the art regardingthe synthesis of disulfide bond containing proteins. The fundamentaldiscovery that a denatured protein, ribonuclease, could assemblecorrectly in the absence of any catalysts indicated that all theinformation for the proper folding of a protein was present in itsprimary amino acid sequence. Since disulfide bonds are necessary for theproper folding of ribonuclease, these experiments were also taken tomean that disulfide bond formation was independent of enzyme catalysts.Thus, it had been presumed that only the presence of oxygen (or smallmolecules such as oxidized glutathione) is needed in vivo for disulfidebond formation. This presumption appeared to explain the fact thatproteins with structural disulfide bonds are only found in the moreoxidizing non-cytosolic intracellular compartments or in theextracellular space. According to this view, disulfide bonds do not formin the cytosol simply because the reducing components such asglutathione and thioredoxins keep such bonds reduced.

The first modification of this view of disulfide bond formation and thebasis for its compartmentalization came from the finding that disulfidebond formation in gram-negative bacteria does require the presence of aprotein catalyst, DsbA (Bardwell, et al. (1991) Cell 67: 581; Kamitani,et al. (1992) EMBO J. 11: 57; Peek, et al. (1992) Proc Natl Acad Sci USA89: 6210; Tomb, J. F. (1992) Proc Nail Acad Sci USA 89: 10252; Yu, etal. (1992) Mol. Microbiol. 6: 1949). This finding not only changed thepicture of how disulfide bond formation takes place normally, but alsoraised questions about the basis for the absence of disulfide bonds incytosolic proteins. Normally, the formation of stable disulfide bonds inthe cytoplasm is an exceedingly rare event (Locker & Griffiths, (1999)J. Cell Biol. 144: 267). Transient disulfide bonds that are not requiredfor the stability of the native state have been detected in a fewcytoplasmic proteins that include enzymes such as ribonucleotidereductase, the transcription factors OxyR and RsrA, the Hsp33 chaperone,and in a partially folded intermediate of the P22 tailspikeendorhamnosidase (Aslund, et al. (1999) Proc Nail Acad Sci USA 96: 6161;Robinson & King (1997) Nat. Struct. Biol. 4: 450; Kang, et al. (1999)EMBO J. 18: 4292 and Jakob et al. (1999) Cell 96:341). In general, theoxidation of cysteine thiols in cytoplasmic proteins is stronglydisfavored for both thermodynamic and kinetic reasons. First of all, thethiol-disulfide redox potential of the cytoplasm is too low to provide asufficient driving force for the formation of stable disulfides. Second,under physiological conditions, there are no enzymes that can catalyzeprotein thiol oxidation. The E. coli cytoplasm contains twothioredoxins, TrxA and TrxC, and three glutaredoxins (Rietsch & Beckwith(1998) Annu. Rev. Genet. 32: 163; Aslund & Beckwith (1999) J. Bacteriol.181: 1375). The oxidized form of these proteins can catalyze theformation of disulfide bonds in peptides. However, in the cytosol boththe thioredoxins and the glutaredoxins are maintained in a reduced stateby the action of thioredoxin reductase (TrxB) and glutathione,respectively. In E. coli, glutathione is synthesized by the gshA andgshB gene products. The enzyme glutathione oxidoreductase, the productof the gor gene, is required to reduce oxidized glutathione and completethe catalytic cycle of the glutathione-glutaredoxin system.

In a trxB null mutant, stable disulfide bonds can form in normallysecreted proteins, such as alkaline phosphatase, when they are expressedin the cytoplasm without a signal sequence. Subsequent studies revealedthat in a trxB mutant, the two thioredoxins are oxidized and serve ascatalysts for the formation of disulfide bonds (Stewart, et al. (1998)EMBO J. 17: 5543). Disulfide bond formation was found to be even moreefficient in double mutants defective in both the thioredoxin (trxB) andglutathione (gor or gshA) pathways (Prinz, et al. (1997) J. Biol. Chem.272: 15661). Double mutants, trxB gor or trxB gshA, grow very poorly(doubling time over 300 minutes) and require an exogenous reductant suchas dithiothreitol (DTT) to achieve a reasonable growth rate.

In view of the numerous proteins of biotechnological and pharmaceuticalinterest, that are complex molecules containing multiple disulfidebonds, such as the tissue plasminogen activator (tPA), it would behighly desirable to have an efficient method of production ofcomplicated proteins which retain their biological activity. Inaddition, since expression of recombinant proteins in bacteria isgenerally a method of choice, but that the formation of disulfide bondsin recombinant proteins expressed in bacteria has been very inefficient,it would be highly desirable to have a prokaryotic system, e.g.,bacterial system that allows efficient expression of recombinantproteins containing multiple disulfide bonds. Such a method would becommercially important, at least in part, to produce therapeutics. Forexample, tPA, is a widely used therapeutic agent with sales exceeding$400 million per year. However, tPA is currently produced in mammaliancells which are costly to grow, resulting in very high price for thedrug (well over $1,000 per dose). Cheaper methods of manufacturingtherapeutic proteins would result in increased availability of the drug,to the benefit of many more patients.

SUMMARY OF THE INVENTION

The invention pertains to compositions and methods for producingproteins of interest containing at least one disulfide bond. Theinvention is based at least in part on the observation that activerecombinant proteins containing a high number of disulfide bonds can beefficiently produced in the cytoplasm of modified prokaryotic cells.

In one embodiment, the invention provides a host cell that isgenetically modified to shift the redox status of its cytoplasm to amore oxidative state. In a preferred embodiment, the host cell furthercontains a gene encoding a catalyst of disulfide bond formation and/orisomerization. The host cell is preferably a prokaryotic cell, but canalso be a eukaryotic cell, e.g., a yeast cell. In a preferredembodiment, the expression or activity of a reductase in the host cellis decreased relative to that in the corresponding wild type cell. Thereductase can be selected from the group consisting of thioredoxinreductase, glutathione reductase, and glutathione. In an even morepreferred embodiment, the expression or activity of a second reductaseis decreased relative to that in the corresponding wild type cell. Thesecond reductase can also be selected from the group consisting ofthioredoxin reductase, glutathione reductase, and glutathione.

In a much preferred embodiment, the gene encoding the reductase ismutated, e.g., the gene contains a null mutation, resulting in thecomplete absence of the gene product. A preferred host cell comprises anull mutation in the thioredoxin reductase gene and in the glutathionereductase gene. Alternatively, the activity of one or more reductases isinhibited, e.g., by contacting the prokaryotic cell with an agent.

In yet another preferred embodiment, the host cell is further modifiedto increase its ability to proliferate. The modification can, e.g.,increase the reducing capacity of the cytoplasm sufficiently to increasethe growth of the host cell. The modification can be a mutation in agene, e.g., a suppressor mutation, or it can an introduction andexpression of a gene encoding a growth promoting protein into the hostcell. In a preferred embodiment, the gene encoding the AphC subunit ofthe alkyl hydroperoxidase is mutated in the host cell, e.g., by thepresence of a mutation in the TCT triplet rich region of the gene (seeFIG. 8A). In another embodiment, a gene encoding a mutated form of AphCis introduced and expressed in the host cell. Such host cells preferablyhave a growth curve that is similar to that of the wild type parentstrain. Particularly preferred host cells are the host cells describedin the Examples, referred to as FA112 and FA113, which are trxB gshasupp and trxB gor supp mutants, respectively. These two strains havebeen deposited at the American Type Culture Collection (ATCC) 10801University Blvd., Manassas, Va. 20110-2209 on Nov. 11, 1999, inaccordance with the terms and provisions of the Budapest Treaty relatingto the deposit of microorganism. FA112 and FA113 have been assigned ATCCAccession No. PTA-938 and PTA-939, respectively.

The host cell can comprise a nucleic acid encoding a catalyst ofdisulfide bondr isomerization, e.g., variants of a thioredoxin orglutaredoxin, which have, e.g., a redox potential that is higher thanthat of its wild type counterpart. In an illustrative example, thevariant is a “Grx” variant of thioredoxin A. The host cell can alsocomprise a catalyst of disulfide bond isomerization, such as a disulfidebond isomerase, e.g., DsbC, or derivative thereof.

In another embodiment, the invention provides a host cell, e.g., aprokaryotic host cell, that is genetically modified to shift is redoxstatus in the cytoplasm to a more oxidative state, and which furthercontains a genetic modification to increase its ability to proliferate.Modification of the oxidative state of its cytoplasm can be achieved bydecreasing the level or activity of one or more reductases, e.g.,thioredoxin reductase, glutathione reductase, and glutathione, asdescribed above. The modification to increase its ability to proliferatecan be a suppressor mutation. Optionally, the host cell can furthercontain a nucleic acid encoding a catalyst of disulfide bond formation.

Also within the scope of the invention are methods for producing aprotein of interest (consisting of one or more polypeptides) having atleast one disulfide bond. The method can comprise introducing into ahost cell, e.g., as described above, a nucleic acid encoding the proteinof interest, growing the host cells in conditions in which the proteinis produced, and isolating the protein from the host cell. This methodis applicable to produce any protein or polypeptide containing at leastone disulfide bond. A person of skill in the art will, of course,recognize that the host cells of the invention can also be used for theproduction of proteins that do not contain any disulfide bonds. Proteinscontaining one or more disulfide bonds are usually secreted or membraneproteins. Thus, the method of the invention is useful for recombinantlyproducing growth or differentiation factors, receptors, secretedenzymes, as well as bacterial and viral proteins. Preferred proteins arethose which have over 1, over 3, over 5, over 10, over 15 or even over20 disulfide bonds.

The proteins and polypeptides, as well as compositions comprising such,are also part of the invention. Such proteins can be used for anypurpose in which recombinant proteins are useful. For example, they canbe used for diagnostic purposes (e.g., as binding agents, such asantibodies), for therapeutic purposes (e.g., tPA) or prophylacticpurposes (e.g., as vaccines). In addition they can be used as foodsupplements, as well as components of wash powders, creams, etc.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic representation of the formation and isomerizationof disulfide bonds (Rietsch and Beckwith (1998), infra).

FIG. 2 is a schematic representation of the thioredoxin and glutaredoxinreducing systems in prokaryotic cells.

FIG. 3 shows the clearing zones obtained from a fibrinolysis assayshowing tPA activity in DHB4 (wild type), WP597 (trxB), FA112 (trxB gshAsupp), and FA113 (trxB gor supp) cells transformed with a plasmidencoding tPA devoid of signal sequence (plasmid pTrcvtPA; top row) or inthe same cells further cotransformed with a “Grx-type” variant TrxA(plasmid pFA5; bottom row).

FIG. 4 is a diagram showing the growth curves of wild type E. coli(DHB4), the trxB gor supp mutant; the trxB gor supp/cytoplasmicvtPA+“Grx-type” TrxA mutant; and the wild type/periplasmic vtPA+DsbCmutant, and the time at which production of vPA was induced.

FIG. 5 shows the amount of biologically active (oxidized, as opposed toreduced) alkaline phosphatase produced in DHB4 (wild type), WP597(trxB), and FA113 (trxB gor supp) transformed with plasmid pAID135,produced during a pulse/chase experiment at 1, 4, or 11 minutespost-chase.

FIG. 6 is a diagram showing the activity of vtPA produced in thecytoplasm of strain FA113 (trxB gor supp) and in FA113 co-transformedwith plasmids pFA2-pFA8, respectively, which encode wild type GrxA(pFA2), wildtype TrxA (pFA3), and active site mutants of TrxA (pFA4-8),relative to the activity of vtPA produced in the cytoplasm of FA113.

FIG. 7 is a diagram showing the activity of vtPA secreted to theperiplasm of DHB4 (wild type), or in the cytoplasm of FA113 (trxB gorsupp) that were cotransformed with plasmids pBADdsbA, pBADdsbC,pBADSSdsbA, pBADSSdsbC, pFA3 (TrxA), and pFA5 (“Grx-type” TrxA).

FIG. 8A shows a portion of the nucleotide sequence and encoded aminoacid sequence of E. coli ahpC gene (amino acids 33 to 48 of GenBankAccession No. BAA02485). The nucleotide sequence of the wild type aphCgene shown corresponds to SEQ ID NO: 8 and the encoded amino acidsequence corresponds to SEQ ID NO: 9. The nucleotide sequence of themutated aphC gene shown corresponds to SEQ ID NO: 10 and the encodedamino acid sequence corresponds to SEQ ID NO: 11. The area of repeatedTCT triplets is highlighed and the additional TCT triplet in AhpC* isframed.

FIG. 8B is an alignment of amino acid sequences of AhpC proteins fromdifferent microorganisms and from the human species (HUMAN_TPA). Thenumbers represent the amino acid position of the first amino acid shownin each protein. The sequences correspond, from top to bottom, to SEQ IDNos: 12-20.

FIG. 9 is a diagam showing the two different forms of AhpC that can befound in a cell depending on the oxidative stress-inducing signal. Theform on the left represents the wil-dtype enzyme and the form on theright, the mutant enzyme.

FIG. 10 is a diagram representing the reduction pathways present in aprokaryotic cell, including AhpCF.

FIG. 11 is a diagram representing the reduction pathways present in aprokaryotic cell in which the gor and trxB genes are biologicallyinactive, and the role that is probably played by AhpCF in such cells.

DETAILED DESCRIPTION OF THE INVENTION

General

The invention pertains to compositions and methods for producingproteins which contain at least one disulfide bond (including anyprotein which, in its mature form does not have a disulfide bond, but aprecursor of which contains a disulfide bond) in a host cell or hostorganism.

In a preferred embodiment, the invention includes modifying thecytoplasm of a host cell to favor proper folding of complex disulfidebond containing proteins, such as by shifting the redox status of thecytoplasm to a more oxidizing status. This host cell of the inventioncan then be used to express a protein of interest in the cytoplasm ofthe host cell. Although the invention pertains mostly to expression ofproteins in the cytoplasm of host cells, a person of skill in the artwill recognize that the techniques described herein can also be appliedto other cellular compartments, e.g., the periplasm. Thus, the instantsystem provides, in particular, for the efficient production ofmammalian proteins having at least one disulfide bond or which have atleast one disulfide bond during their synthesis.

Host cells or organisms of the invention for the efficient production ofdisulfide bond containing proteins can be produced by variousmodifications or combinations of modifications of wild type cells ororganisms or cells or organisms which have already been modified. In oneembodiment, a host cell is modified by reducing or eliminating the levelor activity of one or more reductase in the host cell. In a preferredembodiment, the reductase is selected from the group consisting of thethioredoxin reductase (trxB); glutathione (gshA and gshB); and theglutathione oxidoreductase (gor). Such a host cell can further bemodified to increase its rate of growth, if necessary, such as selectingnaturally occurring mutants, e.g., suppressor mutants, or by theintroduction of a mutation or a heterologous DNA or stimulating theexpression or activity of a gene, thereby resulting in an increasedgrowth rate of the host cell. A modification of a host cell resulting inimproved growth is referred to herein as “growth inducing modification.”Growth of modified host cells can be improved or restored to that ofwild type host cells by increasing the reducing environment of thecytoplasm, preferably without affecting the oxidative environmentnecessary for appropriate oxidation of disulfide bond containingproteins. Accordingly, the oxidizing role of the thioredoxins in thehost cell is preferably not modified. In one embodiment, a modified hostcell is modified by altering the activity of the AphC subunit of thealkyl hydroperoxidase AhpCF, such as by mutating the region of the aphCgene containing four TCT triplets, so that the enzyme has a new reducingactivity. A preferred E. coli bacterial strain having a mutated aphCgene is the strain FA113 which has been deposited at the ATCC and hasbeen assigned ATCC Accession No. PTA-939.

A host cell can further be modified by increasing the level or activityof a catalyst of disulfide bond formation and/or isomerization, such asby overexpressing or stimulating the activity of the DsbC protein or avariant of a thioredoxin (trx) or glutaredoxin (grx) or variant orhomolog thereof. Thus, in one embodiment the invention provides a hostcell, e.g., an E. coli cell, in which the thioredoxin reductase (trxB)and the glutathione oxidoreductase (gor) genes each contain a nullmutation, and the host cell further contains a growth inducingmodification, e.g., a mutation, improving its growth rate, and e.g.,allowing it to grow at a rate similar to that of its wild typecounterpart, such as the E. coli strain having ATCC Accession No.PTA-939 (FA113).

Another preferred embodiment provides an E. coli strain, having a nullmutation in each of the thioredoxin reductase gene (trxB) and in a geneencoding a glutathione biosynthetic enzyme (gshA), and the cell furthercomprises a growth inducing modification, e.g., a mutation, allowing itto grow at essentially the same rate as the corresponding wild-type E.coli strain. A bacterial strain having this genotype has been depositedwith the ATCC and has been assigned ATCC Accession No. PTA-938. Thestrains FA112 and FA113 cells are further described in the Examples. Inanother preferred embodiment, the invention provides an E. coli BL-21trxB gor supp mutant.

In an even more preferred embodiment, a host cell further contains aplasmid encoding the DsbC protein (isomerase). In another embodiment,the host cell containing a null mutation in the thioredoxin reductaseand the glutathione oxidoreductase genes, and optionally a growthinducing modification, further contains at least one plasmid encoding amutant or variant of a thioredoxin or glutaredoxin gene.

In another embodiment, the invention provides a host cell comprising anull mutation in one or more of the thioredoxin reductase (trxB), aglutathione biosynthetic enzyme (gsha and gshB), and the glutathioneoxidoreductase (gor) genes, contains one or more plasmids encoding oneor more catalyst proteins, e.g., DsbC. The host cell may of may notcontain a growth inducing modification, e.g., a mutation. Where the hostcell does not have a growth inducing modificatin, such host cells mayrequire the addition of an agent to their growth media, such as areducing agent.

For purposes of convenience, a list of at least some prokaryoticproteins which are useful in the invention are set forth in Table 1.

TABLE 1 Thiol-disulfide oxidoreductases and their functions Gene redoxGene Product Name Location/Function potential Thioredoxin 1 trxAcytoplasmic reductant; −270 mV reduces dsbC Thioredoxin 2 trxCcytoplasmic reductant Thioredoxin trxB Reduction of thioredoxinsreductase Glutaredoxin 1 grxA cytoplasmic reductant −233 mV Glutaredoxin2 grxB cytoplasmic reductant Glutaredoxin 3 grxA cytoplasmic reductant−198 mV Glutathione gor reduction of oxidized glutathione oxidoreductaseDsbA dsbA periplasmic protein, required for −120 mV disulfide bondformation DsbB dsbB cytoplasmic membrane protein; oxidation of DsbA DsbCdsbC periplasmic protein, required for −130 mV disulfide bondisomerization DsbD (DipZ) dsbD cytoplasmic membrane protein; (dipZ)reduction of DsbC DsbE (CcmG) dsbE cytoplasmic membrane protein, (ccmG)required for cytochrome c biogenesis DsbG dsbG periplasmic protein(Rietsch and Beckwith (1998) Ann. Rev. Genet. 32: 163)

Other modifications or combinations of modifications of host cells aredescribed infra. Although a person of skill in the art will readily beable to predict which modifications or combination of modificationswould result in a host cell that is efficient in the production ofdisulfide containing proteins, various simple methods are available forconfirming this (see, infra).

At least one advantage of synthesizing proteins in the cytoplasm of ahost cell, as opposed to the periplasm, is that the kinetics of proteinoxidation in the cytoplasm are slower than than those in the periplasm.For example, as shown in the Examples (FIG. 4), the half-life for theoxidation of alkaline phosphatase in the cytoplasm is well over aminute, whereas, the protein is nearly fully oxidized within fewer than40 seconds in the periplasm. A slower oxidation rate is likely to bemore favorable because in that case disulfide bond formation is morelikely to be determined by the conformational preferences of thepolypeptide chain which should result in the alignment of the propercysteine residues. Second, the oxidation of proteins in the periplasm byDsbA, a protein required for disulfide bond formation which is naturallypresent only in the periplasm, may be detrimental for the folding ofthose proteins with multiple disulfides. DsbA is a very efficientenzyme; however, it tends to place disulfide bonds in polypeptidesrandomly with little regard for the native conformation. Randomoxidation results in the formation of scrambled disulfides which can bedifficult to rearrange. The addition of reduced glutathione to themedium, rendering the periplasmic space less oxidizing, increases theyield of eukaryotic disulfide-bonded proteins co-expressed in theperiplasm of E. coli with DsbA or rat PDI (Wunderlich, et al. (1993) J.Biol. Chem. 268: 24547; Ostermeier, et al. (1996) J. Biol. Chem. 271:10616). The implication is that somewhat more reducing conditions, thanthose naturally present in the periplasm, facilitate the folding ofeukaryotic proteins containing multiple disulfide bonds. Such conditionscan be found in the cytoplasm of cells, in particular prokaryotic cells.

Furthermore, although some proteins can be expressed in the bacterialperiplasm at high levels (Joly et al. (1998) PNAS 95: 2773), often highlevel secretion, particularly of heterologous proteins, can interferewith the normal function of the Sec pathway causing cell toxicity. Evenoverexpression of homologous proteins can result in cell toxicity, asshown, e.g., in the overexpression of dsbC gene from a strong promoterin FIG. 4. Expression in the cytoplasm, together with, e.g., eithersignal sequenceless DsbC or “Grx-like” variant TrxA, circumvents thisproblem. Thus, not only can complex disulfide bonds be formed morereadily in the cytoplasm, greater cell yields can be achieved as well.

Other aspects of the invention are described below or will be apparentto those skilled in the art in light of the present disclosure.

Definitions

For convenience, the meaning of certain terms and phrases employed inthe specification, examples, and appended claims are provided below. Itis also to be understood that the terminology used herein is for thepurpose of describing particular embodiments only and is not intended tobe limiting.

It must be noted that, as used in the specification and the appendedclaims, the singular forms “a,” “an” and “the” include plural referentsunless the context clearly dictates otherwise. Thus, for example,reference to “a mutation” includes two or more such mutations, and thelike.

The term “oxidation-reduction potential,” used interchangeably hereinwith “redox potential,” of an active site disulfide bond reflectswhether an enzyme is more reducing or oxidizing. In anoxidation-reduction reaction, the atom that increases in oxidationnumber (and thereby loses electrons) is said to undergo oxidation, or tobe oxidized. The atom that is reduced in oxidation number (and therebygains electrons) is said to undergo reduction, or be reduced. Forexample, the redox potential of the endoplasmic reticulumn has beenestimated to be in the range of −172 to −188 mV (Rietsch and Beckwith(1998), infra), based on the ratio of reduced to oxidized glutathione.Table I lists the redox potential of various enzymes.

The term “standard state redox potential” or “E°′” refers to a redoxpotential measured in standard conditions, e.g., in 1M concentration andat pH 7.0.

The term “oxidant” or “oxidizing agent” refers to a compound whichoxidizes molecules in its environment, i.e., which changes the moleculesin its environment to become more oxidized and more oxidizing. Anoxidant acts by accepting electrons, thereby becoming itself reducedafter having oxidized a substrate. Thus, an oxidant is an agent whichaccepts electrons.

The term “oxidizing conditions” or “oxidizing environment” refers to acondition or an environment in which a substrate is more likely tobecome oxidized than reduced. For example, the periplasm of a wild typebacteria constitutes an oxidizing environment, whereas the cytoplasm isa reducing environment.

When referring to an enzyme in an “oxidized state”, it refers to theenzyme having less electrons than its reduced form.

The term “reductant” or “reducing agent” refers to a compound whichreduces molecules in its environment, i.e., which changes molecules inits environment to become more reduced and more reducing. A reducingagent acts by donating electrons, thereby becoming itself oxidized afterhaving reduced a substrate. Thus, a reducing agent is an agent whichdonates electrons. Examples of reducing agents include dithiothreitol(DTT), -mercaptoethanol, cysteine, thioglycolate, cysteamine,glutathione, and sodium borohydride.

The term “reductase” refers to a thioredoxin reductase, glutathione orglutathione reductase (also referred to as “cysteine oxido-reductases)or any other enzyme that can reduce members of the thioredoxin orglutaredoxin systems.

The term “reductase pathways” refers to the systems in cells whichmaintain the environment in reducing conditions, and includes theglutaredoxin system and the thioredoxin system (see FIG. 2).

The term “reducing conditions” or “reducing environment” refers to acondition or an environment in which a substrate is more likely tobecome reduced than oxidized. For example, the cytoplasm of a eukaryoticcell constitutes a reducing environment. The redox potential of thecytoplasm has been estimated to be −260-270 mV (see Hwang et al. (1992)Science 257: 1496).

“Disulfide bond formation” or “disulfide bond oxidation”, usedinterchangeably herein, refers to the process of forming a covalent bondbetween two cysteines present in one or two polypeptides, which isschematized as “—S—S—” (see FIG. 1). Oxidation of disulfide bonds ismediated by thiol-disulfide exchange between the active site cysteinesof enzymes and cysteines in the target protein (see FIG. 1). Disulfidebond formation is catalyzed by enzymes which are referred to ascatalysts of disulfide bond formation.

When referring to an enzyme in a “reduced state”, it refers to theenzyme having more electrons than its oxidized form.

“Disulfide bond reduction” refers to the process of cleaving a disulfidebond, thereby resulting in two thiol groups (—SH groups) (see FIG. 1).Reduction of disulfide bonds is mediated by thiol-disulfide exchangebetween the active site cysteines of enzymes and cysteines in the targetprotein (see FIG. 1).

The term “disulfide bond isomerization” refers to an exchange ofdisulfide bonds between different cysteines, i.e., the shuffling ofdisulfide bonds (see FIG. 1). Isomerization of disulfide bonds ismediated by thiol-disulfide exchange between the active site cysteinesof enzymes and cysteines in the target protein (see FIG. 1) andcatalyzed by isomeras. In E. coli, isomerization is catalyzed by DsbC, aperiplasmic disulfide bond oxidoreductase.

“Protein disulfide bond isomerases” refer to proteins which catalyze theisomerization of disulfide bonds in proteins. Without wanting to belimited to a specific mechanism of action, isomerases are thought to actinitially by invading incorrect disulfide bonds that have been formed inproteins and then allowing or promoting isomerization of the disulfidebond. To carry out this process, it is posited that the two cysteines inteh Cys-Xaa-Xaa-Cys motif must be in the reduced state (FIG. 1). Infact, DsbC is found with its inactive site cysteines in the reducedstate in wild-type E. coli. DsbC is maintained in a reduced state in acell by the cytoplasmic membrane protein DsbD (or DipZ protein).

A “catalyst of disulfide bond formation” is an agent which stimulatesdisulfide bond formation. Such an agent must be in an oxidized state tobe active.

A “catalyst of disulfide bond isomerization”, also referred to as an“disulfide bond isomerase” is an agent which stimulates disulfide bondisomerization. Such an agent must be in a reduced form to be active.

The term “thioredoxin superfamily” refers to the group of enzymescontaining a “thioredoxin fold” which catalyze the reduction, formation,and/or isomerization of disulfide bonds and exert their activity througha redox active disulfide in a Cys-Xaa1-Xaa2-Cys (SEQ ID NO: 1) motif,and includes the thioredoxins, glutaredoxins, DsbA, DsbD, and DsbC.

The term “thioredoxin fold” refers to an overall protein structuralmotif that is shared by the members of the thioredoxin superfamily.Thus, although thioredoxins and glutaredoxins may have relativelydifferent amino acid sequences, they share a similar secondarystructure, i.e., a similar overall fold, referred to as the thioredoxinfold. The thioredoxin fold consists of a central four-strandedbeta-sheet flanked by three alpha-helices in the order (see, e.g., FIG.1 in Jordan et al. (1997), J. Bio. Chem. 272:18044). The thioredoxinfold has been found in five distinct classes of proteins that have thecommon property of interacting with cysteine-containing substrates (see,e.g., Martin J. L. (1995) Structure 3: 245 and Aslund et al. (1996) J.Biol. Chem. 271:6736).

The term “thioredoxin family” includes thioredoxin 1 (trxA), thioredoxin2 (trxC), and thioredoxin reductase (trxB), as described in Rietsch andBeckwith (1998) Ann. Rev. Genet. 32: 163.

The term “thioredoxin” includes thioredoxin 1 (trxA) and thioredoxin 2(trxC), as described in Rietsch and Beckwith (1998) Ann. Rev. Genet. 32:163. Thioredoxins are small proteins characterized by the presence ofthe motif Cys-Xaa-Xaa-Cys (where Xaa denotes any amino acid) in theiractive site. Thioredoxin is re-reduced by thioredoxin reductase (encodedby trxB gene) and NADPH (see FIG. 2). In a trxB mutant, thioredoxinaccumulates in an oxidized form.

The term “glutaredoxin family” includes glutaredoxin 1 (grxA),glutaredoxin 2 (grxB), glutaredoxin 3 (grxC), and glutathioneoxidoreductase (gor), as described in Rietsch and Beckwith (1998) Ann.Rev. Genet. 32: 163.

The term “glutaredoxin” includes glutaredoxin 1 (grxA), glutaredoxin 2(grxB), and glutaredoxin 3 (grxC), as described in Rietsch and Beckwith(1998) Ann. Rev. Genet. 32: 163. Glutaredoxins (encoded by genes termed“grx”, such as grxA, grxB, and grxC genes) which contain theCys-Xaa-Xaa-Cys (SEQ ID NO: 1) (Xaa being any amino acid) active sitemotif, but are distinct from thioredoxins in that they are not reducedby thioredoxin reductase, but by the small tripeptide glutathione, whichitself is reduced by glutathione oxidoreductase (encoded by the gorgene) in the presence of NADPH (see FIG. 2).

The terms “gshA gene” and “gshB gene” refer to the genes encodingglutathione biosynthetic enzymes.

The term “gor gene” refers to the glutathione oxidoreductase gene.

When referring to a protein, the first letter of the name of the proteinis generally a capital letter. When referred to a gene, the first letterof the name of the gene is generally a small cap, and may be,optionally, spelled in italics.

“DsbC”, is a protein encoded by the gene dsbC, which catalyzes disulfidebond isomerization. Certain proteins require DsbC for their folding invivo, e.g., mouse urokinase, bovine pancreatic trypsin inhibitor (BPTI),insulin like growth factor-1, and melanocyte growth stimulating activity(MGSA) (see Rietsch and Beckwith (1998) Ann. Rev. Genet. 32: 163, andreferences cited therein). DsbC null mutants have a defect in thefolding of proteins with multiple disulfide bonds.

“DsbD”, also referred to as “DipZ”, is encoded by the gene dsbD alsoreferred to as dipZ gene, and is a cytoplasmic membrane protein thatmaintains DsbC in a reduced state, i.e., in an active state. DsbD nullmutants have a defect in the folding of proteins with multiple disulfidebonds and causes DsbC to accumulate in an oxidized form, i.e., inactiveform.

“DsbB,” which is encoded by the gene dsbB, is a cytoplasmic proteinwhich oxidizes DsbA. DsbB contains a Cys-Xaa-Xaa-Cys (SEQ ID NO: 1) (Xaabeing any amino acid residue) motif. DsbB may be oxidized by passingelectrons to the restpiratory chain.

“DsbA” is a periplasmic protein required for disulfide bond formationthat is encoded by the gene dsbA.

The term “protein” refers to a single polypeptide or to a complexcomprising at least two (two or more) polypeptides or polypeptidicchains which can be connected by one or more disulfide bond(s).

A “host organism” is intended to encompass a multicellular as well as aunicellular organism. A unicellular host organism is usedinterchangeably with a “host cell”.

A “host cell” is any cell that can be used for the purposes of thisinvention.

When referring to a “modification of host cells,” the term“modification” includes a transient or a permanent alteration of thehost cell, e.g., a constitutive or an inducible alteration. Amodification can be a genetic alteration.

A “growth inducing modification” of a host cells refers to amodification of a host cell resulting in improved or faster growth ofthe host cell. The modification can restore the growth rate of the cellto that of a corresponding wild type host cell, or it can merely improveit. Growth rate of host cells can be determined by counting the cells atdifferent time points, and in the case of prokaryotic host cells, e.g.,by measuring the optical density of a culture (e.g., at about 600 nm) atdifferent time points. A modification can be a mutation of a gene of thehost cell, e.g., a mutation in AphC called AhpC*, or it can be theintroduction of a gene into the host cell, e.g., introduction of a geneencoding AphC*.

As used herein, “signal sequence” or “signal polypeptide” refers to apeptide that directs a polypeptide to be secreted by a cell, to becomemembrane bound or to be secreted into the periplasm of a prokaryoticecell. To assure that a polypepeptide is maintained in the cytoplasm of acell, the signal peptide is removed. Signal peptides have commoncharacteristics, including hydrophobicity, that allows them to beidentified.

An “over-expressed” gene product is one that is expressed at levelsgreater than normal endogenous expression for that gene product. It canbe accomplished, e.g., by introducing a recombinant construction thatdirects expression of a gene product into a host cell, or by alteringbasal levels of expression of an endogenous gene product, e.g., byinducing its transcription.

“Inducible” promoters are promoters which direct transcription at anincreased or decreased rate upon binding of a transcription factor or aninducer. “Transcription factors” as used herein include any factors thatcan bind to a regulatory or control region of a promoter and therebyeffect transcription. The synthesis or the promoter binding ability of atranscription factor within the host cell can be controlled by exposingthe host to an “inducer” or removing an inducer from the host cellmedium. Accordingly, to regulate expression of an inducible promoter, aninducer is added or removed from the growth medium of the host cell.

As used herein, the phrase “to induce expression” means to increase theamount of transcription from specific genes by exposure of the cellscontaining such genes to an effector or inducer.

An “inducer” is a chemical or physical agent which, when given to apopulation of cells, will increase the amount of transcription fromspecific genes. These are usually small molecules whose effects arespecific to particular operons or groups of genes, and can includesugars, phosphate, alcohol, metal ions, hormones, heat, cold, and thelike. For example, isopropylthio-beta-galactoside (IPTG) and lactose areinducers of the taclI promoter, and L-arabinose is a suitable inducer ofthe arabinose promoter. The pho gene promoter, such as phoA and pho5, isinducible by low phosphate concentrations in the medium.

As used herein, a “protein or polypeptide of interest” refers generallyto a protein or polypeptide which can be expressed in the host cell andrecovered from the host cell. Preferably such a polypeptide comprises atleast about 5 amino acids, preferably at least about 10 amino acids, 15amino acids, 20 amino acids, 25, 30, 35, 40, 50, 100 amino acids or morethan 120 amino acids.

The term “containing at least one disulfide bond” when referring to aprotein or polypeptide refers to a protein or polypeptide which has adisulfide bond in its mature form and/or in a precursor form.

A “heterologous protein or polypeptide” refers to a protein orpolypeptide which is not normally produced in the host cell. Aheterologous polypeptide can be from the same species and type as thehost cell provide that it is expressed from a nucleic acid which hasbeen introduced into the host cell.

The phrase “hydrophobic residues” refers to the residues norleucine,cysteine, methionine, alanine, valine, leucine, tyrosine, phenylalanine,tryptophan, and isoleucine.

The expression “control sequences” refers to DNA sequences necessary forthe expression of an operably linked coding sequence in a particularhost organism. The control sequences that are suitable for bacteriainclude a promoter such as the alkaline phosphatase promoter, optionallyan operator sequence, and a ribosome-binding site.

A nucleic acid is “operably linked” to another nucleic acid when it isplaced into a functional relationship with another nucleic acidsequence. For example, DNA for a presequence or secretory leader isoperably linked to DNA for a polypeptide if it is expressed as apreprotein that participates in the secretion of the polypeptide; apromoter or enhancer is operably linked to a coding sequence if itaffects the transcription of the sequence; or a ribosome binding site isoperably linked to a coding sequence if it is positioned so as tofacilitate translation. Generally, “operably linked” means that the DNAsequences being linked are contiguous and, in the case of a secretoryleader, contiguous and in reading phase. Linking is accomplished byligation at convenient restriction sites. If such sites do not exist,the synthetic oligonucleotide adaptors or linkers are used in accordancewith conventional practice.

As used herein, the expressions “cell,” “cell line,” and “cell culture”are used interchangeably and all such designations include progeny.Thus, the words “transformants” and “transformed cells” include theprimary subject cell and cultures derived therefrom without regard forthe number of transfers. It is also understood that all progeny may notbe precisely identical in DNA content, due to deliberate or inadvertentmutations. Mutant progeny that have the same function or biologicalactivity as screened for in the originally transformed cell areincluded. Where distinct designations are intended, it will be clearfrom the context.

“Production phase of cell growth” refers to the period of time duringcell growth following induction of the promoter when the polypeptide ofinterest is being produced.

“Plasmids” for use in the invention include those which becomeintegrated into the host cell genome and those which are autonomouslyreplicating plasmids.

The “Km” of an enzyme refers to the Michaelis constant of the enzymewhich is equal to the substrate concentration at which the reaction rateis half its maximal value (Vmax). The Km of an enzyme can be determinedby methods known in the art. Typical Km values range from 10⁻¹ to 10⁻⁶M.

The term “k” or “Kcal” refers to the rate constant in an enzymaticreaction.

The term “AhpCF” refers to the alkyl hydrogen peroxide reductase, alsoreferred to herein as alkyl hydroperoxide reductase which comprises twosubunits (see FIG. 9). AhpC is the smaller subunit and the other subunitis the flavoenzyme AhpF (Tarataglia et al, J. Biol. Chem., Volume 265,10535-10540, 1990; Smillie et al, Genbank submission NCBL gi; 216542,1993). This enzymatic complex (or system) scavenges oxygen and itsderivatives. The AhpC protein contains the peroxide reducing catalyticsite, which is centered around amino acid 47 (cysteine) in the E. colienzyme (SEQ ID NO: 22), and the ahpF protein is an NAD(P)Hdehydrogenase. Oxygen stress responses involving AhpC homologs arehighly conserved in bacteria, yeast, parasites and even in vertebrates(Chae et al, J. Biol. Chem., Volume 269, 27670-27678, 1994; Tsuji et al,Biochem. J., Volume 307, 377-381, 1995; Armstrong-Buisseret et al,Microbiology-UK, Volume 141, 1655-1661, 1995; Bruchhaus et al, Molecularand Biochemical Parasitology, Volume 70, 187-191, 1995; Ferrante et al,PNAS, USA, Volume 92, 7617-7621, 1995; Wilson et al, Mol. Microbiol.,Volume 19, 1025-1034, 1996; and FIG. 8B).

Host Cells and Organisms of the Invention

The invention generally is applicable to any host organism of host cellwhich is capable of expressing heterologous polypeptides, and which canpreferably be genetically engineered. A host organism is preferably aunicellular host organism, however, multicellular organisms are alsoencompassed in the invention, provided the organism can be modified asdescribed herein and a polypeptide of interest expressed therein. Forpurposes of clarity, the term “host cell” will be used hereinthroughout, but it should be understood, that a host organism can besubstituted for the host cell, unless unfeasable for technical reasons.In a preferred embodiment the host cell is a prokaryotic cell. Inanother embodiment, the host cell is a eukaryotic cell, such as a yeastcell or a mammalian cell. In an even more preferred embodiment, the hostcell is a bacterial cell, preferably a gram negative bacterial cell,e.g., an E. coli bacteria.

The host organisms can be aerobic or anaerobic organisms.

Preferred host cells are those which have characteristics which arefavorable for expressing polypeptides, such as host cells having fewerproteases than other types of cells. Thus, for example, host cells whichhave been modified to reduce the level or activity of proteases can beused, e.g., BL-21 (see below).

Other preferred bacterial strains have been modified to become lysogenicfor the T7 (DE3) phage, allowing for expression of proteins using thepET series of plasmids.

Suitable bacteria for this purpose include archaebacteria andeubacteria, especially eubacteria, and most preferablyEnterobacteriaceae. Other examples of useful bacteria includeEscherichia, Enterobacter, Azotobacter, Erwinia, Bacillus, Pseudomonas,Klebsiella, Proteus, Salmonella, Serratia, Shigella, Rhizobia,Vitreoscilla, and Paracoccus. Suitable E. coli hosts include E. coliDHB4, E. coli BL-21 (which are deficient in both lon (Phillips et al.(1984) J. Bacteriol. 159: 283.) and ompT proteases), E. coli AD494, E.coli W3110 (ATCC 27,325), E. coli 294 (ATCC 31,446), E. coli B, and E.coli X1776 (ATCC 31,537). Other strains include E. coli B834 which aremethionine deficient and, therefore, enables high specific activitylabeling of target proteins with ³⁵S-methionine or selenomethionine(Leahy et al. (1992) Science 258, 987). Yet other strains of interestinclude the BLR strain, and the K-12 strains HMS174 and NovaBlue, whichare recA-derivative that improve plasmid monomer yields and may helpstabilize target plasmids containing repetitive sequences (these strainscan be obtained from Novagen).

These examples are illustrative rather than limiting. Mutant cells ofany of the above-mentioned bacteria may also be employed. It is, ofcourse, necessary to select the appropriate bacteria taking intoconsideration replicability of the replicon in the cells of a bacterium.For example, E. coli, Serratia, or Salmonella species can be suitablyused as the host when well known plasmids such as pBR322, pBR325,pACYC177, or pKN410 are used to supply the replicon.

E. coli strain W3110 is also a preferred host because it is a commonhost strain for recombinant DNA product fermentations. Preferably, thehost cell should secrete minimal amounts of proteolytic enzymes. Forexample, strain W3110 may be modified to effect a genetic mutation inthe genes encoding proteins, with examples of such hosts including E.coli W3110 strain 1A2, which has the complete genotype tonA DELTA (alsoknown as DELTA fhuA); E. coli W3110 strain 9E4, which has the completegenotype tonA DELTA ptr3; E. coli W3110 strain 27C7 (ATCC 55,244), whichhas the complete genotype tonA DELTA ptr3 phoA DELTA E15 DELTA(argF-lac)169 ompT DELTA degP41kan^(R) ; E. coli W3110 strain 37D6,which has the complete genotype tonA DELTA ptr3 phoA DELTA E15 DELTA(argF-lac)169 ompT DELTA degP41kan^(R) rbs7 DELTA ilvG; E. coli W3110strain 40B4, which is strain 37D6 with a non-kanamycin resistant degPdeletion mutation; E. coli W3110 strain 33D3, which has the completegenotype tonA ptr3 lacIq LacL8 ompT degP kan^(R) ; E. coli W3110 strain36F8, which has the complete genotype tonA phoA DELTA (argF-lac) ptr3degP kan^(R) ilvG⁺, and is temperature resistant at 37° C.

The host cells of the invention can be stored, e.g., as glycerol stocks,which can be prepared according to known methods of the invention.

Modification of Host Cells to Favor Disulfide Bond Formation in theirCytoplasm

In one embodiment the invention provides a host cell having a cytoplasmthat favors disulfide bond formation in proteins. Since normally thecytoplasm of a cell is composed of an essentially reducing environment,which disfavors disulfide bond formation, the host cell is, e.g.,modified to shift the redox state of its cytoplasm to more oxidizingconditions. This can be achieved, e.g., by altering one or morereductase pathways in the host cell. Thus, in an illustrativeembodiment, the invention comprises modifying one or more of thefollowing two reductase systems existing, in particular, in prokaryoticcells: the thioredoxin/thioredoxin reductase pathway (the “thioredoxinsystem”) and the glutathione/glutaredoxin pathway (the “glutaredoxinsystem”; see FIG. 2). The thioredoxin system consists of the thioredoxinreductase enzyme (TrxB) which reduces a thioredoxin (TrxA or TrxC) whichthen reduce substrate proteins. The glutaredoxin system consists of theglutathione reductase (also referred to as “glutathione oxidoreductase”;Gor) which reduces glutathione (GshA and GshB) which reduces aglutaredoxin (GrxA, GrxB, or GrxC) which then reduces substrate proteins(see, e.g., Rietsch and Beckwith (1998) Ann. Rev. Genet. 32: 163).

In a preferred embodiment of the invention, the cytoplasmic redox statusof the cytoplasm of a host cell is increased (i.e., the redox status ofthe cytoplasm becomes a more oxidizing environment) by inhibiting ordecreasing the activity or level of a reductase, such as the thioredoxinreductase (trxB), glutathione (gshA or gshB), or glutathione reductase(gor). In a preferred embodiment, expression of the reductase iseliminated, i.e., reduced to zero or to undetectable levels, byinactivating the gene encoding the reductase according to methods wellknown in the art and further set forth below. Thus, preferred host cellsare completely devoid of the expression of a reductase, such as thethioredoxin reductase, glutathione, or the glutathione reductase. Inanother embodiment, expression of a reductase is inducible, i.e., it isexpressed only in the presence or absence of a certain inducer. Forexample, a reductase can be expressed under the control of an arabinosepromoter (further described herein). Accordingly, the reductase will beexpressed only in the presence of arabinose, and not in its absence. Anull phenotype is then created by cultivating the host cells in theabsence of arabinose. Such a system also allows the control of theamount of reductase that is made in the host cell. When using aninducible reductase gene, it may be desirable to use a host cell whichis devoid of the wild type reductase gene (see Examples).

In yet another embodiment the expression of a reductase in a host cellis reduced by inhibiting the transcription of the gene encoding thereductase, by degrading the RNA encoding the reductase, or by inhibitingtranslation of the RNA. Transcription and translation can be inhibitedby introducing into, or expressing antisense nucleic acids in the hostcell. Alternatively, these processes can be inhibited by contacting thehost cells with small organic molecules which interfere with theseprocesses. Such compounds can be identified, e.g., in screening assays.It will be understood that the expression of a reductase in a host cellcan also be reduced or eliminated by modulating the expression of one ormore proteins that control the expression of the reductase in the hostcell by acting upstream of the reductase gene in its regulation. Forexample, expression of a reductase can be decreased by reducing theexpression or activity of a factor that is necessary for the expressionof the reductase.

Instead of, or in addition to, inhibiting or decreasing the level of thereductase protein in a host cell, the activity of, the reductase can bereduced or eliminated. In a particular embodiment, the host cell isincubated with a compound that inhibits the activity of a reductase,e.g., the thioredoxin reductase, glutathione, or the glutathionereductase. Such compounds can be identified in screening assays, bymethods known in the art.

Alternatively, reductase expression can be prevented by the use ofconstructs that would allow the turning on of a protease to degrade thereductase. This can be done, e.g., by inserting a protease sensitivesite in the reductase (see, e.g., Ehrman et al. (1997) PNAS 94:13111)

Preferred host cells of the invention fail to express, or have decreasedexpression or activity of the thioredoxin reductase (trxB) and one ormore of the glutathione (gshA or gshB) and glutathione reductase (gor).Accordingly, a preferred host cell of the invention is a prokaryoticcell having a null mutation in trxB and a null mutation in gshA or ingor. As previously described, such double mutants may grow poorly, andit may be necessary to add a reductant, such as DTT, to their culturemedium. In an illustrative example, an amount of DTT ranging from about1 to 10 mM, preferably from about 2 to 4 mM, is appropriate to increasethe growth of these cells. When a trxB gor or trxB gshA strain is grownin medium containing DTT and then transferred to medium lacking DTT, thecytoplasm becomes even more oxidizing than in the trxB strain, resultingin the accumulation of high levels of alkaline phosphatase or mouseurokinase activity (Prinz, et al. (1997) J. Biol. Chem. 272: 15661).

In conditions in which one does not desire to add DTT in the culturemedium, one can use any of the above-described host cells in which theexpression of one or more reductase genes is inducible. Alternatively,the host cells may be modified by the introduction of a growth inducingmodification, e.g., by introducing a mutation (see below).

Gram positive prokaryotic cells, e.g., Bacillus, are known not topossess the glutaredoxin system. Thus, the redox status of the cytoplasmis reduced simply by reducing or eliminating the expression or activityof the reductase of the thioredoxin system. If the elimination of areductase is lethal to the host cells, it may be necessary to renderexpression of the reductase inducible, such as by methods furtherdescribed herein.

Modification of Host Cells to Obtain Favorable Growth

As set forth above, modification of a host cell that results in improveddisulfide bond formation in the cytoplasm, such as by changing the redoxpotential of its cytoplasm, in particular, where the cytoplasm isrendered more oxidizing, the growth and survival of the cell may beaffected. For example, a bacteria having a null mutation in thethioredoxin reductase gene and a null mutation in either of aglutathione gene or the glutathione reductase gene grows much morepoorly than its wild type counterpart or even a single mutant havingonly one of these null mutations. As described in the Examples, growthof such cells can be improved by the addition in the growth medium of areductant, such as DTT.

Alternatively, the growth of cells can be rescued by the selection ofsuppressor mutants, such as described in the Examples. In anillustrative embodiment, suppressor mutants are selected by growingcells in the presence of DTT for a certain time period, removing DTTfrom the culture media, and selecting fast growing colonies. Forexample, cells can be grown for 24 hours in the presence of 6 mM DTT.Fast growing cells can the isolated and diluted suspensions of thesecells can then be plated to isolate single colonies. The growth rate ofbacteria can be determined according to methods well known in the art.

Suppressor mutants can have mutations in any gene that compensates forthe lack of growth due to null mutations in reductases. The mutation maybe a loss of function mutation or a gain of function mutation. It is notnecessary to know in which gene the suppressor mutation occurred inorder to practice the invention. However, it might be of interest toknow the identity of the mutation for increasing the growth rate ofother strains of host cells without having to select for suppressormutants, but simply by creating the same mutation as that in thesuppressor mutant.

Several methods exist for determining the identity of the suppressorgene. For example, transposons can be mapped by linkage analysis, asdescribed, e.g., in Kleckner et al. (1991) Meth. Enzym. 204:139.Alternatively, suppressor mutants can be obtained by random insertion ofDNA into the host cell chromosome and sequencing the DNA of the hostcell that is flanking the DNA inserted into the genome of the host cell,using primers which bind to the DNA insert. Such techniques are wellknown in the field of prokaryotic genetics.

The rapid growth of a trxB gor supp strain (FA113, see Examples)indicates that bacteria can tolerate large perturbations in theircytoplasmic thiol-disulfide redox potential. This implies that the vastmajority of native cytoplasmic proteins in FA113 are unable to formaberrant disulfides, even under oxidizing conditions. Thus, suppressormutations are likely to be capable of saving any host cell engineered asdescribed herein from slow growth. More generally, suppressor mutationscan be introduced into a strain to cure any type of defect or change acharacteristic of a cell, in addition to increasing its growth rate.

As described in the Examples, the suppressor mutation in strain FA113has been localized to the gene ahpC, encoding the small catalyticsubunit of the alkyl hydroperoxidase, AhpCF, which catalyses thedestruction of oxidative species, e.g., peroxidase. The mutationcorresponds to the addition of a triplet within the region of the genecontaining four TCT triplets (see FIG. 8A), which is a region whichcontains the cysteine (amino acid 47) that is located in the catalyticsite of the enzyme. A nucleic acid encoding this mutated form of AhpC isset forth in SEQ ID NO: 23, and the amino acid encoded therefrom is setforth in SEQ ID NO: 24. The wild type nucleic acid and amino acids ofAhpC are set forth in SEQ ID NO: 21 and 22, respectively, and correspondto GenBank Accessions Nos. D13187 (Feb. 3, 1998) and BAA02485 (Feb. 3,1998), respectively. As further described in the Examples, this mutationessentially destroys the peroxidase activity of the enzyme. As furthershown herein, the presence of mutated AhpC (referred to as AhpC*)provides growth enhancing capability to host cells only in the presenceof AhpF and of a functional glutaredoxin system. Thus, it is likely thatAhpC* enhances growth by reducing oxidized glutaredoxin 1 orglutathione. Generally, it is believed that the AhpC* increases thereducing capacity to the cytoplasm sufficient to allow growth.

Accordingly, growth of host cells can also be improved by introducing amodification in the host cell which increases the reducing capacity ofits cytoplasm. The modification can be a mutation in a gene of the hostcell, e.g., a mutation which increases the reducing potential of anenzyme, or which reduces the oxidizing potential of an enzyme. Apreferred modification is a mutation in the AphC gene, e.g., a mutationin its catalytic domain. An even more preferred mutation is one thatoccurs in the TCT triplet repeat, such as the insertion of a TCTtriplet, as shown in FIG. 8A. A preferred mutant AhpC has the amino acidsequence set forth in SEQ ID NO: 24. Other mutations can also be made toAhpC, provided that the mutation improves the growth of the cells.Identification of other mutations, e.g., in AhpC, that have a growthimproving activity can be identified, e.g., by introducing randommutations in a host cell, e.g., one having mutations in trxB and in gor,and selecting for those having enhanced growth. The mere culture of suchmutated cells will result in an enriched population of cells havinggrowth inducing mutations, which can then be identified. Randommutations can be introduced and identified according to methods wellknown in the art of prokaryotic genetics.

As opposed to introducing a mutation in a particular gene to inducegrowth, one may also downregulate the expression of the gene by any of avariety of methods, including antisense expression or the contacting thecell with an agent that reduces transcription of the gene.

Alternatively, the modification of host cells can be the introductioninto the host cell of a gene which enhances growth or stimulating theexpression of a gene enhancing growth in the host cell. For example, ahost cell can be modified by the introduction into the cell of a geneencoding a protein which increases the reducing capacity of thecytoplasm. In a preferred embodiment, the gene is a reductase. In aneven more preferred embodiment, the gene encodes AhpC*. The gene can bemaintained episomally or the gene can be integrated into the chromosome.It may be desirable, in certain circumstances to reduce or elimate theamount of the corresponding protein of the growth inducing gene. In thecase in which a gene encoding AhpC* is introduced into a cell, andoptionally overexpressed, it is not necessary to reduce expression ofthe wild type gene encoding AhpC, since it has been shown herein thatAhpC* is dominant.

In view of the strong conservation of the AhpC genes across species(see, e.g., FIG. 8B), host cells other than E. coli can be modified in asimilar fashion to improve their growth potential. For example, a hostcell can be modified by introducing a gene encoding a mutated AhpCprotein, such as one having a mutation in the repeated triplet region.

It is likely that the reason the trxB,gor and trxB,gshA strains do notgrow is that they do not have sufficient reducing power to maintain theessential enzyme ribonucleotide reductase in the reduced, active state.Accordingly, another class of suppressors that may restore growth tothese strains is one in which one (or more) of the severalribonucleotide reductase genes on the E. coli chromosome is altered bymutation so that it no longer needs the thioredoxin orglutathione/glutaredoxin pathways as a source of reducing power. Itwould obtain its electrons from one of the other possible sources in thecytoplasm. Such suppressor strains may, in addition, be even moreefficient at disulfide bond formation than the strains having a mutationin ahpC because, in contrast to the likely consequence of the ahpCmutation, these suppressor mutations do not generate any new reducingpower. The cytoplasm may well be more oxidizing vis-a-vis disulfidebonds than FA113.

Modification of Host Cells by the Addition of Genes Encoding Catalystsof Disulfide Bond Formation and/or Isomerization

As shown in the Examples, proper folding of polypeptides comprisingnumerous disulfide bonds expressed in host cells was increased bycotransformation of the host cell with a catalyst of disulfide bondformation and/or a catalyst of disulfide bond isomerization. Thus,generally the invention provides host cells which are modified toover-express or increase the activity of one or more catalyst(s) ofdisulfide bond formation and/or isomerization.

In a preferred embodiment, a catalyst of disulfide bond formation is anenzyme which facilitates, or increases the speed of, disulfide bondformation. Generally, a catalyst of disulfide bond formation will havethe following characteristics: it is able to accumulate in oxidized formin the cytoplasm, and the oxidized form of the protein catalyst isefficient at transferring its disulfide to a substrate protein.Accordingly, since a catalyst of disulfide bond formation must be inoxidized form in the cytoplasm to be active, the catalyst will generallyhave a low redox potential, e.g., in the range of the redox potential ofthe thioredoxins and glutaredoxins. Thus, catalysts of disulfide bondformation will preferably have a redox potential of at most about −270mV, preferably at most about −260 mV, at most about −250 mV, at mostabout −240 mV, at most about −230 mV, at most about −220 mV, at mostabout −210 mV, at most about −200 mV, or at most about −190 mV. Otherpreferred catalysts have a redox potential in the range of about −260 to−190 mV, more preferably, of about −230 to −190 mV, and even morepreferably of about −210 to −190 mV. However, catalysts of disulfidebond formation can also have a redox potential outside of these ranges,provided that the enzyme is capable of catalyzing disulfide bondformation, as can be shown in in vitro or in vivo assays, as further setforth herein.

Catalysts of disulfide bond isomerization are enzymes which are capableto form disulfide bonds, but which are also capable of shufflingdisulfide bonds. Generally, catalysts of disulfide bond isomerizationwill be in a reduced state in the cytolasm, so that they are capable ofinvading incorrectly formed disulfide bonds. Accordingly, an isomerasewill generally have a higher redox potential than a catalyst ofdisulfide bond formation. Preferred isomerases have a redox potential ofat most about −200 mV, at most about −190 mV, at most about −180 mV,preferably at most about −170 mV, preferably at most about −160 mV, andmost preferably at most about −150 mV. However, an isomerase can alsohave a redox potential outside of these ranges, provided that the enzymeis capable of catalyzing isomerization of disulfide bonds, which can bedemonstrated in vitro or in vivo, as further set forth hererin.

A preferred catalyst of disulfide bond isomerization of the invention isDsbC or an variant of homolog thereof. Thus, a host cell of theinvention, such as a host cell in which the activity or level ofexpression of a reductase enzyme is decreased or eliminated, can betransformed with a gene encoding DsbC. As further described in theExamples, co-expression of DsbC (having a redox potential of −130 mV) ina host cell resulted in a dramatic increase in the production ofdisulfide bond containing proteins.

In an illustrative embodiment, the gene encoding DsbC is constitutivelyexpressed, i.e., under the control of a constitutive promoter.Alternatively, the gene can be inducible, i.e., under the control of aninducible promoter. In the later situation, DsbC can the be induced,e.g., upon the addition to the culture medium of the inducer. Induciblepromoters are further described herein.

Generally, where the catalyst of the invention is a protein which isnormally expressed in the periplasm or is secreted, expression of thecatalyst in the cytoplasm of the host cell requires that the signalsequence be deleted.

Other preferred catalysts of the invention are proteins or compoundswhich regulate the expression or activity of a catalyst, e.g., DsbC. Forexample, disulfide bond formation can be stimulated in a host cell byoverexpressing the cytoplasmic membrane protein DsbD (DipZ), whichreduces DsbC, and thereby augments DsbC's activity to function as anisomerase. Alternatively, the activity of DsbD can be increased, e.g.,by inducing its reduction.

Another catalyst that can be used in certain circumstances include theprotein DsbA, which increases disulfide bond formation. DsbA has beenshown in vitro to be an extremely efficient catalyst of disulfide bondformation (see Rietsch and Beckwith (1998) infra). This property isconsistent with the high redox potential of its active site disulfidebond. DsbA oxidizes its substrates by transferring the disulfide bondfrom its active site to the target protein. Overexpression of thisprotein, or stimulation of its activity, is preferably used forexpressing proteins containing a low number of disulfide bonds, e.g., asingle disulfide bond, rather than proteins containing high number ofdisulfide bonds. It has, in fact, been reported that DsbA promotes theformation of incorrect disulfide bonds in substrate proteins containingmultiple disulfide bonds. Thus, when expressing complicated proteins ina host cell which overexpresses DsbA or in which its activity isstimulated, it may be desirable to overexpress or stimulate the activityof a disulfide bond isomerase, e.g., the isomerase DsbC.

The activity of DsbA can be stimulated by overexpressing or stimulatingthe activity of an enzyme which oxidizes DsbA. Indeed, after catalyzingdisulfide bond formation, DsbA is left in a reduced state, and theactive site disulfide bond must be reoxidized in order for DsbA tocatalyze another round of disulfide bond formation. Reoxidation of DsbAis performed by the integral membrane protein DsbB. Thus, activation ofDsbA can be done by overexpressing, or stimulating the activity of, theprotein DsbB.

In yet another embodiment, the activity or level of thioredoxins orglutaredoxins is increased in the host cell. It has been shown thatthioredoxins, which under normal, i.e., wild type cytoplasmic conditionsact as potent reductases, can in fact act as oxidants when present inoxidizing conditions, such as in a cytoplasm in which the expression ofone or more of the reductases thioredoxin reductase, glutathione, andglutathione reductase is inhibited (Stewart et al. (1998) EMBO J.17:5543). Also, as described in the Examples, co-expression of wild typethioredoxin (−270 mV) increased disulfide bond formation. Thus, theseproteins will stimulate disulfide bond formation in host cells whichfail to express wild type amounts of one or more reductase. Accordingly,overexpression of one or more of thioredoxins or glutaredoxins willincrease the production of correctly folded proteins comprising at leastone disulfide bond.

Although wild-type thioredoxin and glutaredoxin enzymes can be used ascatalysts in the methods of the invention, preferred catalysts includemutant versions of these enzymes that are more effective at promotingdisulfide bond formation and/or isomerization than their wild typecounterparts. For example, a variant of thioredoxin (trxA), that is moreoxidizing than its wildtype counterpart, can be expressed in a hostcell. As described further herein, the redox potential of most cysteineoxidoreductases, including TrxA, is strongly influenced by the sequenceof the dipeptide within the C-Xaa-Xaa-C (SEQ ID NO: 1) active site motif(Mossner, et al. (1999) J. Biol. Chem. 274: 25254; Mossner, et al.(1998) Protein Sci. 7: 1233; Grauschopf, et al. (1995) Cell 83: 947). Asshown in the Examples, co-expression of more oxidizing TrxA variants(higher redox potential) resulted in higher expression of the disulfidebond containing proteins. Indeed, the efficiency of disulfide bondformation was markedly increased by introducing plasmids expressingthioredoxin mutant proteins poised at a higher redox potential, thantheir wild type counterparts. Preferred thioredoxin or glutaredoxinvariants include those that are mutated in the active site of theenzyme, i.e., in the C-Xaa-Xaa-C (SEQ ID NO: 1) sequence. The variantcan have an amino acid substitution, deletion or addition. Preferredvariants include -CGSC- (SEQ ID NO: 3); -CPYC- (SEQ ID NO: 4), which isthe active site found in wild type Grx proteins, and which is referredto herein as the “Grx-like” variant; --CPHC- (SEQ ID NO: 5), which isthe active site found in the wild type DsbA protein, and which isreferred to herein as the “DsbA-like” variant; and -CGHC- (SEQ ID NO:6), which is the active site found in the wild type rat proteindisulfide isomerase (PDI) and which is referred to herein as the“PDI-like” thioredoxin mutant. The redox potential of these mutants havebeen estimated from the equilibrium constants with glutathione solutionsto be −195 mV, −204 mV and −221 mV, respectively, i.e., higher than the−270 mV of the wild type thioredoxin (Mossner et al. (1998) Protein Sci.7:1233).

Without wanting to be limited to a specific mechanism of action, it isbelieved that the variants of thioredoxin are more potent catalysts thanthe wildtype counterpart, since their redox potential are higher thanthat of the wildtype thioredoxin (−270 mV). This difference in redoxpotential likely results in wild type thioredoxin being fully oxidized,as it has been observed, whereas the higher redox potential variantswere found to accumulate predominantly in reduced form, which can thenserve as a catalyst for disulfide bond isomerization.

Accordingly, preferred thioredoxin or glutaredoxin variants for use ascatalysts in the invention comprise a redox potential of at most about−270 mV, preferably at most about −260 mV, at most about −250 mV, atmost about −240 mV, at most about −230 mV, at most about −220 mV, atmost about −210 mV, at most about −200 mV, or at most about −190 mV.Other preferred catalysts have a redox potential in the range of about−260 to −190 mV, more preferably, of about −230 to −190 mV, and evenmore preferably of about −210 to −190 mV. However, a variant can alsohave a redox potential outside of these ranges, provided that thevariant is capable of catalyzing isomerization of disulfide bonds, whichcan be demonstrated in vitro or in vivo, as further set forth herein.

The redox potential of a protein can be determined by various methods,such as by calculation from the equilibrium constant of the redoxreaction involving a reference with known redox potential using theNernst equation. The commonly used references are definedglutathione/glutathione disulfide (GSH/GSSG) buffers or NADPH/NADP+coupled via an appropriate reductase (Gilbert H. F. (1990) Adv. Enzymol.Relat. Areas Mol. Biol. 63:69). Another method is set forth in Krause etal. (1991) J. Biol. Chem. 299: 9494. A preferred method for determiningredox potentials of proteins, e.g., members of thioredoxin superfamilyand variants thereof, is described in Aslund et al. (1997) J. Biol.Chem. 272: 30780 and in Mossner et al. (1998) Prot. Sci. 7:1233.Briefly, this method of pair-wise equilibration described in Aslund etal. (1997) for obtaining E°′ is based on accurate determinations of theequilibrium constant, K₁₂ for the reversible thiol-disulfide exchangereaction between various pairs of redox active proteins. Standard stateredox potentials are then obtained through equilibration with knownstandards, e.g., either Trx“PDI” or Trx, whose redox potential has beendetermined independently (Krause et al. (1991) J. Biol. Chem. 266:9494)via coupling to NADPH (E°′=−315 mV).

In certain cases, the redox potential of a protein is linked to its pKavalue. For example, in the case of DsbA, a linear correlation betweenredox potential and the pKa value of the nucleophilic thiol of theactive site has been demonstrated (Krause et al. (1991) J. Biol. Chem.266:9494). Apparently, a major function of the active site motif(CX1X2C) is to modulate the pKa value of the nucleophilic thiol andthereby the stability of the reduced form of the protein relative to theoxidized form. Thus, in the case of DsbA, the very low pKa value of 3.5(Nelson et al. (1994) Biochemistry 33:5974) is an important factor forits highly oxidizing properties. Accordingly, the identification of aprotein, e.g., a thioredoxin variant, having oxidizing properties may beidentified by the selection of a variant having a low pKa value. The pKacan be determined by methods known in the art, and described, e.g., inNelson et al., supra.

When expressing variants of wild-type thioredoxin and glutaredoxinenzymes, it may be desirable to inactivate or to inhibit thecorresponding endogenous wildtype enzymes in the host cell. This ispreferably achieved by introducing null mutations into the correspondingwild type genes. Alternatively, this can be achieved by including intothe growth medium of the host cells, a compound which blocks theirexpression or their activity.

Another catalyst of disulfide bond formation that can be used in theinvention is the protein disulfide isomerase (PDI), which is a proteinwhich catalyzes disulfide bond formation in eukaryotes. PDI has beenimplicated in the catalysis of disulfide bond formation andrearrangement through in vitro data (Creighton et al. (1980) J. Mol.Biol. 142:43; Feedman et al. (1989) Biochem. Soc. Symp. 5:167; andBardwell and Beckwith (1993) Cell 74:899. Yeast mutants in PDI have beenshown to have a defect in the formation of disulfide bonds incarboxypeptidase Y (LaMantia and Lennarz (1993) Cell 74:899). Use of PDIfor expression of heterologous proteins in host cells is furtherdescribed in PCT application having publication No. WO 93/25676; WO94/08012; and EP 509,841. A variant PDI which can also be used in thisinvention is disclosed in EP 293,793.

Yet another protein or derivative thereof that can be used as a catalystin the invention is the glutaredoxin-like protein NrdH, present in,e.g., E. coli, Lactocuccus Lactis, and Salmonella typhimurium, describedin Jordan et al. (1997) J. Biol. Chem. 272:18044. This enzyme is reducedby thioredoxin reductase, but not by glutathione.

Homologs, variants, and in particular, enzymes of interest can beobtained from various species or genuses by hybridization techniques orusing cross-reacting antibodies. It is known that catalysts of disulfidebond formation and isomarization are relatively well conserved amongspecies, and one could thus, using a sequence from one species, clonethe sequence from another species. Appropriate stringency conditionswhich promote DNA hybridization, for example, 6.0× sodiumchloride/sodium citrate (SSC) at about 45° C., followed by a wash of2.0×SSC at 50° C., are known to those skilled in the art or can be foundin Current Protocols in Molecular Biology, John Wiley & Sons, N.Y.(1989), 6.3.1-6.3.6. For example, the salt concentration in the washstep can be selected from a low stringency of about 2.0×SSC at 50° C. toa high stringency of about 0.2×SSC at 50° C. In addition, thetemperature in the wash step can be increased from low stringencyconditions at room temperature, about 22° C., to high stringencyconditions at about 65° C. Both temperature and salt may be varied, ortemperature of salt concentration may be held constant while the othervariable is changed. In a preferred embodiment, a nucleic acid of thepresent invention will bind to that of another species under moderatelystringent conditions, for example at about 2.0×SSC and about 40° C.

Additional catalysts of disulfide bond formation and/or isomerizationcan be isolated, e.g., by identifying additional substrates ofreductases, e.g., thioredoxin reductase and glutathione oxidoreductase.Additional variants of known substrates of reductases and catalysts ofdisulfide bond formation can be can be identified and prepared by avariety of methods known in the art. These methods include, but are notlimited to, in vivo methods, as well as the following in vitro methods:preparation by oligonucleotide-mediated (or site-directed) mutagenesis,alanine-scanning mutagenesis, random mutagenesis, PCR mutagenesis, andcassette mutagenesis of an earlier prepared variant or a wild typeprotein. Alternatively, such variants can be isolated by screening of alibrary of variants.

In designing variants, it may be useful to align the sequence of themembers of the thioredoxin superfamily, e.g., as shown in Jordan et al.,supra, and in FIG. 2 of Aslund et al. (1996) J. Bio. Chem. 271: 6736.The knowledge of the redox potential, and other characteristics of theseenzymes will then allow the determination of which amino acid should beconserved and of those amino acids which can be modified to maintain, oralternatively modify certain characteristics of a member of the family.In particular, as further described herein, modification of theC-Xaa-Xaa-C (SEQ ID NO: 1) active site of a member is likely to affectits redox potential. The effect of the modifications on the redoxpotential can be determined as further described herein, and in Aslundet al. (1997) supra. Variants having a specific characteristic, e.g., aspecific redox potential, can be screened for.

In a preferred embodiment, a thioredoxin variants having an enhancedactivity are identified by in vivo techniques, e.g., in vivo geneticscreens for selection of mutants that are enhanced. Such methods cancomprise looking for those variants which when expressed oroverexpressed in a host cell enhance the production of properly foldedtest protein, e.g., tPA.

Set forth below are in vitro methods for modifying thioredoxin familymembers or catalysts. Oligonucleotide-mediated mutagenesis represents apreferred method for preparing substitution, deletion, and insertionvariants of genes, although other methods may be utilized as desired.This technique is well known in the art as described by Zoller andSmith, Nucleic Acids Res., 10: 6487 (1982). Briefly, DNA is altered byhybridizing an oligonucleotide encoding the desired mutation to a DNAtemplate, where the template is the single-stranded form of a plasmid orbacteriophage containing the unaltered or native DNA sequence. Afterhybridization, a DNA polymerase is used to synthesize an entire secondcomplementary strand of the template that will thus incorporate theoligonucleotide primer, and will code for the selected alteration in theDNA.

Generally, oligonucleotides of at least 25 nucleotides in length areused. A preferred oligonucleotide will have 12 to 15 nucleotides thatare completely complementary to the template on either side of thenucleotide(s) coding for the mutation. This ensures that theoligonucleotide will hybridize properly to the single-stranded DNAtemplate molecule. The oligonucleotides are readily synthesized usingtechniques known in the art such as that described by Crea et al., Proc.Natl. Acad. Sci USA, 75: 5765 (1978). The DNA template can be generatedby those vectors that are either derived from bacteriophage M13 vectors(the commercially available M13 mp18 and M13 mp19 vectors are suitable),or those vectors that contain a single-stranded phage origin ofreplication as described by Viera et al., Meth. Enzymol., 153: 3 (1987).Thus, the DNA that is to be mutated may be inserted into one of thesevectors to generate single-stranded template. Production of thesingle-stranded template is described in Sections 4.21-4.41 of Sambrooket al., Molecular Cloning: A Laboratory Manual (Cold Spring HarborLaboratory Press, NY 1989). Alternatively, a single-stranded DNAtemplate may be generated by denaturing double-stranded plasmid (orother) DNA using standard techniques.

A useful method for identification of certain residues or regions of aprotein, such a thioredoxin, glutaredoxin, isomerase or other catalystof disulfide bond formation that are preferred locations for mutagenesisis called “alanine-scanning mutagenesis,” as described by Cunningham andWells, Science, 244: 1081-1085 (1989). Here, a residue or group oftarget residues are identified (e.g., charged residues such as arg, asp,his, lys, and glu) and replaced by a neutral or negatively charged aminoacid (most preferably alanine or polyalanine) to affect the interactionof the amino acids with the surrounding aqueous environment in oroutside the cell. Those domains demonstrating functional sensitivity tothe substitutions then are refined by introducing further or othervariants at or for the sites of substitution. Thus, while the site forintroducing an amino acid sequence variation is predetermined, thenature of the mutation per se need not be predetermined. For example, tooptimize the performance of a mutation at a given site, alanine scanningor random mutagenesis is conducted at the target codon or region and theexpressed variants are screened for the most preferred combination ofdesired activity.

For alteration of the native DNA sequence (to generate amino acidsequence variants, for example), the preferred method is the combinationof oligonucleotide-directed mutagenesis and random mutagenesis asdescribed by Kunkel et al., Methods Enzymol., 154: 367 (1987). In thismethod, oligonucleotide-directed mutagenesis is employed to randomizeparticular codons of the wild-type gene to encode all possible residues.A pool of oligonucleotides with complementary sequence (about 10-15bases) flanking the codon of choice is used. The codon of choice isreplaced with the nucleotides NNS, where N is any nucleotide and S is Gor C, to give a pool of oligonucleotides encoding all possible aminoacids in 32 codons.

In this preferred method, a pBR322-derived plasmid with asingle-stranded origin of replication is prepared as a single-strandedplasmid template in an E. coli dut-ung-strain such as CJ236 (Kunkel etal., supra). These two mutations in the strain cause the incorporationof one or more uracil nucleotides into the single-stranded DNA insteadof thymine. The random oligonucleotides are annealed, filled in with E.coli phage T7 DNA polymerase, ligated, and transformed into a wild-typestrain of E. coli such as W3110 or strain 13G8 (W3110 tonA DELTAPhoS64). The latter strain is negative for the particular gene andderived from CGSC6777 (C75-b), which is derived from C75, described byAmemura et al., J. Bacter., 152: 692-701 (1982). The wild-type straincorrects the uracil misincorporation using the synthetic mutant strandas a template so as to produce about 90% mutants.

DNA encoding mutants with more than one amino acid to be substituted maybe generated in one of several ways. If the amino acids are locatedclose together in the polypeptide chain, they may be mutatedsimultaneously using one oligonucleotide that codes for all of thedesired amino acid substitutions. If, however, the amino acids arelocated some distance from each other (separated by more than about tenamino acids), it is more difficult to generate a single oligonucleotidethat encodes all of the desired changes. Instead, one of two alternativemethods may be employed.

In the first method, a separate oligonucleotide is generated for eachamino acid to be substituted. The oligonucleotides are then annealed tothe single-stranded template DNA simultaneously, and the second strandof DNA that is synthesized from the template will encode all of thedesired amino acid substitutions. The alternative method involves two ormore rounds of mutagenesis to produce the desired mutant. The firstround is as described for the single mutants: wild-type DNA is used forthe template, an oligonucleotide encoding the first desired amino acidsubstitution(s) is annealed to this template, and the heteroduplex DNAmolecule is then generated. The second round of mutagenesis utilizes themutated DNA produced in the first round of mutagenesis as the template.Thus, this template already contains one or more mutations. Theoligonucleotide encoding the additional desired amino acidsubstitution(s) is then annealed to this template, and the resultingstrand of DNA now encodes mutations from both the first and secondrounds of mutagenesis. This resultant DNA can be used as a template in athird round of mutagenesis, and so on.

PCR mutagenesis is also suitable for making amino acid variants of athioredoxin, glutaredoxin, DsbC or other catalyst of disulfide bondformation and/or isomerization. While the following discussion refers toDNA, it is understood that the technique also finds application withRNA. The PCR technique generally refers to the following procedure (seeErlich, supra, the chapter by R. Higuchi, p. 61-70): When small amountsof template DNA are used as starting material in a PCR, primers thatdiffer slightly in sequence from the corresponding region in a templateDNA can be used to generate relatively large quantities of a specificDNA fragment that differs from the template sequence only at thepositions where the primers differ from the template. For introductionof a mutation into a plasmid DNA, one of the primers is designed tooverlap the position of the mutation and to contain the mutation; thesequence of the other primer must be identical to a stretch of sequenceof the opposite strand of the plasmid, but this sequence can be locatedanywhere along the plasmid DNA. It is preferred, however, that thesequence of the second primer is located within 200 nucleotides fromthat of the first, such that in the end the entire amplified region ofDNA bounded by the primers can be easily sequenced. PCR amplificationusing a primer pair like the one just described results in a populationof DNA fragments that differ at the position of the mutation specifiedby the primer, and possibly at other positions, as template copying issomewhat error-prone.

If the ratio of template to product material is extremely low, the vastmajority of product DNA fragments incorporate the desired mutation(s).This product material is used to replace the corresponding region in theplasmid that served as PCR template using standard DNA technology.Mutations at separate positions can be introduced simultaneously byeither using a mutant second primer, or performing a second PCR withdifferent mutant primers and ligating the two resulting PCR fragmentssimultaneously to the vector fragment in a three (or more)-partligation.

Another method for preparing variants, cassette mutagenesis, is based onthe technique described by Wells et al., Gene, 34: 315 (1985). Thestarting material is the plasmid (or other vector) comprising the DNA tobe mutated. The codon(s) in the DNA to be mutated are identified. Theremust be a unique restriction endonuclease site on each side of theidentified mutation site(s). If no such restriction sites exist, theymay be generated using the above-described oligonucleotide-mediatedmutagenesis method to introduce them at appropriate locations in theDNA. After the restriction sites have been introduced into the plasmid,the plasmid is cut at these sites to linearize it. A double-strandedoligonucleotide encoding the sequence of the DNA between the restrictionsites but containing the desired mutation(s) is synthesized usingstandard procedures. The two strands are synthesized separately and thenhybridized together using standard techniques. This double-strandedoligonucleotide is referred to as the cassette. This cassette isdesigned to have 3′ and 5′ ends that are compatible with the ends of thelinearized plasmid, such that it can be directly ligated to the plasmid.This plasmid now contains the mutated DNA sequence.

Nucleic acid encoding the variant may also be chemically synthesized andassembled by any of a number of techniques, prior to expression in ahost cell. (See, e.g., Caruthers, U.S. Pat. No. 4,500,707; Balland etal., Biochimie, 67: 725-736 (1985); Edge et al., Nature, 292: 756-762(1982)).

A DNA variant typically may be made by random and/or site-specificmutagenesis of the native-encoding nucleic acid and transfection orintegration of the variant gene into the chromosomes of a bacterialhost, or by random mutagenesis of a host containing the native gene. Thenucleic acid variant may then be screened in a suitable screening assayfor the desired characteristic.

Catalysts of disulfide bond isomerization must be in a reduced state tobe active and must be able to reduce a substrate. Several methods can beused to determine whether an enzyme is capable of reducing a substrate,or more specifically reduce the disulfide bond(s) of a substrate. Theseare set forth below.

The reducing capacity of an enzyme, e.g., a thioredoxin variant, can bemeasured using the beta-hydroxyethylene disulfide (HED) reduction assay(Holmgren et al. (1979) J. Biol. Chem. 254, 3664).

Another method for determining the reducing capacity of an enzyme is bythe in vitro reduction of insulin disulfides, which can be monitoredspectrophotometrically as described previously (Luthman and Holmgren(1982) J. Biol. Chem. 257:6686 and Moessner et al. (1999) J. Biol. Chem.274: 25254). Briefly, bovine pancreas insulin (Sigma, finalconcentration 0.1 mM) is added to cuvettes containing 0.5 ml of 1 mMGSH, 0.2 mM NADPH, 10 μg/ml glutathione reductase, 0.1 mg/ml bovineserum albumin, and 50 mM Tris-Cl at pH 8.0. The reaction is started bythe addition of the different enzymes to be assayed and monitored bymeasuring the consumption of NADPH at 340 nm for 10 min at 25° C.

Alternatively, the reducing capacity of an enzyme is determined in aRibonucleotide Reductase Activity, as described, e.g., in Thelander etal., (1978) Methods Enzymol. 51: 227, and Holmgren (1979) J. Biol. Chem.254: 9113, by monitoring the conversion of [³H]CDP to [³H]dCDP by 10 μgof ribonucleotide reductase. Reducing equivalents can be providedthrough 4.0 mM GSH, 1.0 mM NADPH, and 0.01 mg/ml glutathione reductase.Incubations are performed in the presence of either 1.0 μM Grx1 or 0.35μM Grx3.

Other substrates that can be used for determining the reducing capacityof an enzyme include lipoic acid and oxidized DTT. Such assays aredescribed, e.g., in Moessner et al. (1999) J. Biol. Chem. 274: 25254.

Several methods can be used to assess disulfide bond isomerization invitro. In an illustrative embodiment, the disulfide bond isomerizationcapability of an enzyme is measured by the ability of the enzyme toisomerize a misoxidized form of bovine pancreatic trypsin inhibitor(BPTI) (Zapun et al. (1995) Biochemistry 34: 5075).

Assays for determining the ability of an enzyme to catalyze theformation of disulfide bonds are set forth, e.g., in Zapun and Creighton(1994) Biochemistry 33: 5202 and Jonda et al. (1999) EMBO J. 18: 3271.Typically, an enzyme and a reduced substrate are incubated together andthe amount of reduced and oxidized substrates is determined, e.g., HPLCor Mass Spectrometry. A substrate protein is, e.g., a ribonuclease orhirudin.

Characteristics of enzymes, e.g., the K_(M) (Michaelis Menten constant),Vmax, Kcat, and kcat/K_(M), can be determined according to methods knownin the art, e.g., as described in Moessner et al. (1999) J. Biol. Chem.274: 25254. Preferred enzymes have a K_(M) with a substrate of with areductase which reduces them, of at least about 10⁻¹ M⁻¹, preferably atleast about 10⁻² M⁻¹, at least about 10⁻³ M⁻¹, at least about 10⁻⁴ M⁻¹,at least about 10⁻⁵ M⁻¹, at least about 10⁻⁶ M⁻¹, and most preferably atleast about 10⁻⁷ M⁻¹. Preferred enzymes, e.g., thioredoxin variants,have a rate constant (kcat) in a reaction with a substrate or areductase that reduces them, of about 40 s⁻¹ or less, preferably 35 s⁻¹or less, preferably 30 s⁻¹ or less, preferably 25 s⁻¹ or less,preferably 20 s⁻¹ or less, preferably 15 s⁻¹ or less, preferably 10 s⁻¹or less, or even more preferably 5 s⁻¹ or less. Preferred enzymes have akat/K_(M) of about 10⁷ M⁻¹ s⁻¹, or about 1,5×10⁷, about 2×10⁷, or about2.5×10⁷.

Secondary structure analysis using NMR can be performed as described inAslund et al. (1996) J. Biol. Chem. 271: 6736.

Several of the assays described in this section require the use ofisolated protein, e.g., a thioredoxin variant or a reductase, such asobtained by in vitro production. Preparation and purification of theseenzymes are described in numerous articles, including articles citedherein.

Additional Modifications to the Host Cells

Host cells of the invention can further be modified to improve thesynthesis or folding of the polypeptides of interest.

In one embodiment, a host cell is further modified to express achaperone protein, which assists in the folding of the protein ofinterest. A chaperone can be, for example, a heat-shock protein, such asthe heat-shock sigma factor, e.g., the heat-shock factor sigma₃₂ encodedby the gene rpoH (Wulfing and Pluckthun (1994) Mol. Microbiol. 12:685).For example, Wulfing and Pluckthun have produced functional fragments ofthe T cell receptor (TCR) in the periplasm of E. coli by overproductionof this heat-shock factor. WO 94/08012 also describes the describes theproduction of a heterologous protein by coexpressing of a chaperone,such as a heat-shock factor. Another heat shock factor which can becoexpressed for its chaperone properties, is Hsp33, a member of the heatshock family of proteins (Jakob et al. (1999) Cell 96:341).

Methods and Materials for Modifying Host Cells

A person of skill in the art will readily know how to modify host cells,such as prokaryotic cells, e.g., E. coli cells, to obtain the host cellsdescribed herein, according to methods in prokaryotic genetics.Similarly, methods for expressing polypeptides in host cells are wellknown in the art. Furthermore some partially modified host cells can becommercially purchased. For example, Novagen makes available variousbacterial strains containing a null mutation in the trxA and/or the trxBgenes. For example, Novagen strain AD494 lacks the thioredoxin reductase(trxB) gene.

The nucleotide and amino acid sequences of the genes to be mutated, oroverexpressed in a host cell are publicly available, e.g., in GenBank,and are described in numerous references. Nucleic acids to be mutated oroverexpressed and host cells, such as bacterial strains, can be obtainedat the ATCC, or can be purchased from commercial vendors, e.g, Novagen.

However, for simplicity, methods of producing modified prokaryotic cellsare briefly set forth below.

A nucleic acid (e.g., cDNA or genomic DNA) encoding a protein ofinterest, a catalyst, or chaperone, or other protein can be suitablyinserted into a replicable vector for expression in the prokaryotic cellunder the control of a suitable prokaryotic promoter. Many vectors areavailable for this purpose, and selection of the appropriate vector willdepend mainly on the size of the nucleic acid to be inserted into thevector and the particular host cell to be transformed with the vector.Each vector contains various components depending on its function(amplification of DNA or expression of DNA) and the particular host cellwith which it is compatible. The vector components for bacterialtransformation generally include, but are not limited to, one or more ofthe following: a signal sequence, an origin of replication, one or moremarker genes, and an inducible promoter.

In general, plasmid vectors containing replicon and control sequencesthat are derived from species compatible with the host cell are used inconnection with bacterial hosts. The vector ordinarily carries areplication site, as well as marking sequences that are capable ofproviding phenotypic selection in transformed cells. For example, E.coli is typically transformed using pBR322, a plasmid derived from an E.coli species (see, e.g., Bolivar et al., Gene, 2: 95 (1977)). pBR322contains genes for ampicillin and tetracycline resistance and thusprovides easy means for identifying transformed cells. The pBR322plasmid, or other microbial plasmid or phage, also generally contains,or is modified to contain, promoters that can be used by the microbialorganism for expression of the selectable marker genes.

The DNA encoding the polypeptide of interest herein may be expressed notonly directly, but also as a fusion with another polypeptide, such as apolypeptide from the host cell.

Both expression and cloning vectors contain a nucleic acid sequence thatenables the vector to replicate in one or more selected host cells.Generally, in cloning vectors this sequence is one that enables thevector to replicate independently of the host chromosomal DNA, andincludes origins of replication or autonomously replicating sequences.Such sequences are well known for a variety of bacteria. The origin ofreplication from the plasmid pBR322 is suitable for most Gram-negativebacteria.

Expression and cloning vectors also generally contain a selection gene,also termed a selectable marker. This gene encodes a protein necessaryfor the survival or growth of transformed host cells grown in aselective culture medium. Host cells not transformed with the vectorcontaining the selection gene will not survive in the culture medium.Typical selection genes encode proteins that (a) confer resistance toantibiotics or other toxins, e.g., ampicillin, neomycin, methotrexate,or tetracycline, (b) complement auxotrophic deficiencies, or (c) supplycritical nutrients not available from complex media, e.g., the geneencoding D-alanine racemase for Bacilli. One example of a selectionscheme utilizes a drug to arrest growth of a host cell. Those cells thatare successfully transformed with a heterologous gene produce a proteinconferring drug resistance and thus survive the selection regimen.

The expression vector for producing a heterologous polypeptide orcatalyst of disulfide bond formation and/or isomerization may alsocontain an inducible promoter that is recognized by the host bacterialorganism and is operably linked to the nucleic acid encoding thepolypeptide of interest or the catalyst. Inducible promoters suitablefor use with bacterial hosts include the beta-lactamase and lactosepromoter systems (Chang et al., Nature, 275: 615 (1978); Goeddel et al.,Nature, 281: 544 (1979)), the arabinose promoter system (Guzman et al.,J. Bacteriol., 174: 7716-7728 (1992)), alkaline phosphatase, atryptophan (trp) promoter system (Goeddel, Nucleic Acids Res., 8: 4057(1980) and EP 36,776) and hybrid promoters such as the tac promoter(deBoer et al., Proc. Natl. Acad. Sci. USA, 80: 21-25 (1983)). However,other known bacterial inducible promoters are suitable. Their nucleotidesequences have been published, thereby enabling a skilled workeroperably to ligate them to DNA encoding the polypeptide of interest orthe catalyst encoding genes (Siebenlist et al., Cell, 20: 269 (1980))using linkers or adaptors to supply any required restriction sites.

Promoters for use in bacterial systems also generally contain aShine-Dalgarno (S.D.) sequence operably linked to the DNA encoding thepolypeptide of interest. The promoter can be removed from the bacterialsource DNA by restriction enzyme digestion and inserted into the vectorcontaining the desired DNA.

Construction of suitable vectors containing one or more of theabove-listed components employs standard ligation techniques. Isolatedplasmids or DNA fragments are cleaved, tailored, and re-ligated in theform desired to generate the plasmids required.

For analysis to confirm correct sequences in plasmids constructed, theligation mixtures can be used to transform E. coli K12 strain 294 (ATCC31,446) or other strains, and successful transformants can be selectedby ampicillin or tetracycline resistance where appropriate. Plasmidsfrom the transformants can be prepared, analyzed by restrictionendonuclease digestion, and/or sequenced by the method of Sanger et al.,Proc. Natl. Acad. Sci. USA, 74: 5463-5467 (1977) or Messing et al.,Nucleic Acids Res., 9: 309 (1981) or by the method of Maxam et al.,Methods in Enzymology, 65: 499 (1980).

Host cells are transfected, and preferably transformed with theabove-described expression vectors of this invention and cultured inconventional nutrient media modified as appropriate for inducing thevarious promoters.

Transfection refers to the taking up of an expression vector by a hostcell whether or not any coding sequences are in fact expressed. Numerousmethods of transfection are known to the ordinarily skilled artisan, forexample, CaCl₂ and electroporation. Successful transfection is generallyrecognized when any indication of the operation of this vector occurswithin the host cell.

Transformation means introducing DNA into an organism so that the DNA isreplicable, either as an extrachromosomal element or by chromosomalintegrant. Depending on the host cell used, transformation is done usingstandard techniques appropriate to such cells. The calcium treatmentemploying calcium chloride, as described in section 1.82 of Sambrook etal., Molecular Cloning: A Laboratory Manual [New York: Cold SpringHarbor Laboratory Press, 1989], is generally used for bacterial cellsthat contain substantial cell-wall barriers. Another method fortransformation employs polyethylene glycol/DMSO, as described in Chungand Miller, Nucleic Acids Res., 16: 3580 (1988). Yet another method isthe use of the technique termed electroporation.

In an exemplary embodiment, insertion of a gene of interest or a geneencoding a catalyst of disulfide bond formation and/or isomerizationinto the host genome includes using a vector for transformation whichcontains a DNA sequence that is complementary to a sequence found in thegenonmic DNA of the host cell. Transfection of the host cell, e.g., E.coli, with this vector results in homologous recombination with thegenome and insertion of the gene. As a result of the transformation, thehost cell is either negative for that particular gene (is a null mutantof that particular gene) or has its wild-type gene replaced by a variantgene upon integration thereof. Accordingly, the same technique can alsobe used to mutate a particular gene in a host cell, i.e., to obtain anull mutant of that gene.

Assays for Determining the Efficiency of the Host Cells in ProducingProperly Folded Proteins Having at Least One Disulfide Bond

Various methods for determining the extent of proper disulfide bondformation in the cytoplasm of a bacteria can be used. In one method, thebacteria are transformed with a gene encoding a polypeptide (a “test”polypeptide) which normally contains at least one disulfide bond.Preferred test polypeptides or proteins are those which are normallysecreted from cells or which are membrane proteins. For use in theassays described herein, these polypeptides are modified by the deletionor mutation of the signal sequence, such that the proteins are notexported outside of the cytoplasm of the cell.

Preferably the test comprises expressing a complicated polypeptide,i.e., having multiple disulfide bonds, e.g., tPA or urokinase (seeExamples). Preferably, the test polypeptide lacks a biological activitywhen it does not have properly formed disulfide bonds. For example,alkaline phosphatase and urokinase proteins require disulfide bonds tobe active. Thus, when these proteins are expressed in the cytoplasm ofwild type bacteria, no disulfide bonds are formed, and these proteinsare not active. Biological activity tests for these proteins arecommercially available (see Examples).

If desired, various methods can be used to determine whether a gene ofinterest is expressed in a host cell. For example, expression of theprotein can be determined by conventional Northern blotting toquantitate the transcription of mRNA. Various labels may be employed,most commonly radioisotopes. However, other techniques may also beemployed, such as using biotin-modified nucleotides for introductioninto a polynucleotide. The biotin then serves as the site for binding toavidin or antibodies, which may be labeled with a wide variety oflabels, such as radionuclides, fluorescers, enzymes, or the like.

Moreover, when antibodies reactive against a given gene product areavailable, such antibodies can be used to detect the gene product in anyknown immunological assay (e.g., as in Harlowe et al., Antibodies: ALaboratory Manual, Cold Spring Harbor Laboratory Press, New York, 1988).The gene product can also be detected using tests that distinguishpolypeptides on the basis of characteristic physical properties such asmolecular weight. To detect the physical properties of the gene product,all polypeptides newly synthesized by the host cell can be labeled,e.g., with a radioisotope. Common radioisotopes that can be used tolabel polypeptides synthesized within a host cell include tritium (³H),carbon-14 (¹⁴C), sulfur-35 (³⁵S), and the like. For example, the hostcell can be grown in ³⁵S-methionine or ³⁵S-cysteine medium, and asignificant amount of the ³⁵S label will be preferentially incorporatedinto any newly synthesized polypeptide, including the over-expressedheterologous polypeptide. The ³⁵S-containing culture medium is thenremoved and the cells are washed and placed in fresh non-radioactiveculture medium. After the cells are maintained in the fresh medium for atime and under conditions sufficient to allow secretion of the³⁵S-radiolabeled expressed heterologous polypeptide, the culture mediumis collected and separated from the host cells. The molecular weight ofthe secreted, labeled polypeptide in the culture medium can then bedetermined by known procedures, e.g., polyacrylamide gelelectrophoresis. Such procedures, and/or other procedures for detectingsecreted gene products, are further described in the Examples, and arealso provided in Goeddel, D. V. (ed.) 1990, Gene Expression Technology,Methods in Enzymology, Vol. 185 (Academic Press), and Sambrook et al.,supra.

A factor which may predict the ability of a modified host cell toproduce disulfide bond containing proteins is the redox potential of thecytoplasm of the host cell. There are currently many different methodsto measure cellular redox status, e.g., as described in Gilbert et al.(1990) Adv. Enzymol. Rel. Areas Mol. Biol. 63:69; Holmgren and Fgestedt(1982) J. Biol. Chem. 257: 6926; and Hwang et al. (1992) Science 257:1496.

Exemplary Methods of Practicing the Invention

In an illustrative embodiment, disulfide bond containing proteins of theinvention are produced as follows. A host cell or organism of theinvention is first transformed with an expression plasmid encoding apolypeptide of interest and a selection marker. The plasmid can encodeadditional polypeptides, such as is desired, e.g., in the production ofmulti-polypepeptide proteins. Additional plasmids encoding otherpolypeptides can be co-transformed, or transformed separately into thehost cell or ogranism. When using more than one plasmid, it may bepreferable to use different markers of selection, to insure that all thedesired plasmids are contained in the recombinant host cell that isselected. Following transformation of the one or more plasmids into thehost cells, according to known methods, clones having taken up theplasmid(s) are selected on appropriate medium, and cloned. Separateclones are then tested to confirm that they have the desiredcharacteristics, including the expression of the one or morepolypeptides. In particular, the polypeptide(s) of interest can beisolated from the host cells, and tested for activity, amount, etc. Theisolated clones can then be frozen in aliquots for preservation,pursuant to methods well known in the art.

Once a clone of the host cell expressing the protein of interest hasbeen obtained, the cloned host cell can be grown in large cultures toproduce large amounts of the protein of interest, from which thepolylpeptide(s) of interest can be isolated.

The polypeptide of interest can, e.g., be produced by growing the hostcells expressing the protein of interest in shaker flasks, as described,e.g., in Qui et al. (1998) Appl. Environ. Microbiol. 64:4891. Briefly,the host cells containing a plasmid encoding the protein of interest aregrown in Luria-Bertani medium at 37° C. supplemented with selectiondrugs, e.g., amplicillin (100 μg/ml), kanamycin (40 μg/ml), andchloramphenicol (20 μg/ml). The synthesis of a protein whose expressionis under the control of an inducible promoter (e.g., the protein ofinterest or a catalyst of disulfide bond formation) can then be inducedby the addition of an inducer, e.g., IPTG (2 mM final) when the cultureoptical density at 600 nm (OD₆₀₀) reached between 0.8 and 1.0. Afterinduction, cultures are grown for approximately three more hours, andthe harvested by centrifugation. The cells can then be resuspended in0.1 M Tris-HCl (pH 8.5) and lysed with a French pressure cell operatedat 2,000 lb/in². Subsequently the cell lysates can be centrifuged at12,000×g for about 10 minutes at 4° C. to separate the soluble andinsoluble fractions.

The polypeptide of interest can also be produced in fermentators, asdescribed, e.g., in Qui et al. (1998) Appl. Environ. Microbiol. 64:4891.Briefly, 1 ml of frozen host cells containing a plasmid encoding theprotein of interest are used to inoculate 500 ml of Luria-Bertani mediumcontaining the appropriate antibiotic. The culture is grown in a 2 literflask for 10 hours, reaching an OD₅₅₀ of about 3.0. This inoculumculture is then added to approximately 6.5 liters of mineral saltsmedium containing 1.2% digested casein, 1.2% yeast extract, and 1.5 g ofisoleucine and 1 g of glucose per liter in a 15 liter Biolafitefermentor. The fermentor is operated at 37° C. and 1,000 rpm, with 10standard liters per minute of aeration and a 0.3 bar back pressure todeliver an oxygen transfer rate of approximately 3.0 mmol/liter-min.When the initial glucose was depleted, a concentrated glucose solutioncan be added to maintain a growth rate of 0.32 h⁻¹ until the dissolvedoxygen concentration (DO₂) reached 30% of air saturation. At that pointglucose feeding is adjusted to maintain a DO₂ of 30%. At an OD₅₅₀ of 25,a feed consisting of 13.5% digested casein and 6.5% yeast extract isadded at 0.5 m./min. When the OD₅₅₀ reaches 80, IPTG or other inducer(if needed) is added at a concentration of 0.05 mM, and other inducers,e.g., arabinose (0.1% final) can be added, as needed. When respirationpoisoning causes the DO₂ to rise, the glucose feed rate can be loweredto avoid excessive acetate accumulation.

A method for isolating the protein of interest, e.g., tPA, from theculture of host cells is described in Qui et al. (1998), supra. Methodsfor quantitating tPA activity is also described in Qui et al. (1998),supra.

The host cells of the invention are preferably capable of producing aproperly folded protein of interest to a level that is at least two foldhigher, at least 3 fold, at least 5 fold, at least 10 fold, at least 20fold, at least 50 fold, 100 fold higher, at least 10⁴, 10⁵, 10⁶ or morefold higher relative to the production of properly folded protein in theperiplasm of the same cell or relative to its production in the wildtypecell or in a partially modified cell (i.e., a cell that has only some ofthe modifications, e.g., null mutations, or inserted genes).

Other methods, assays, and materials that may be useful in practicingthe invention are provided in the literature, in particular, in thefollowing references: Debarbieux and Beckwith (1998) PNAS 95: 10751; Quiet al. (1998) Applied Environm. Microbiol. 64: 4891; Derman et al.(1993) Science 262: 1744; Prinz et al. (1997) J. Biol. Chem. 272: 15661;Stewart et al. (1998) EMBO J. 17: 5543; Aslund et al. (1999) PNAS 274:25254; and Moessner et al. (1999) J. Biol. Chem. 274: 25254.

Polypeptides and Compositions of the Invention

The invention provides polypeptides expressed in heterologous host cellsmodified as described herein to produce high levels of properly foldedpolypeptides or proteins having at least one disulfide bond. Inaddition, since certain proteins, which do not have disulfide bonds whenthey are completely synthesized, pass through an intermediate structurehaving at least one disulfide bonds (see Background of the Invention),the instant invention is also useful for producing such proteins. Thepolypeptides can also have at least 2, at least 3, 4, 5, 6, 7, 8, 9, 10,12, or 15 disulfide bonds, or more. However, as shown herein, theinvention can also be used in producing proteins having at least 17disulfide bridges, at least 20, at least 25, or at least 30 disulfidebridges. The system of the invention can efficiently produce properlyformed and active proteins having any number of disulfide bonds. Thesystem of the invention can also be used for the production of proteinshaving multiple polypeptide chains that are linked through one or moredisulfide bonds.

The polypeptides of the invention are preferably at least about 30%pure, at least about 40%, 50%, 60%, 70%, 80%, 90%, or even morepreferably at least about 95% pure. Yet, even more preferredpolypeptides of the invention are at least 97%, 98%, or 99% pure. Thepurity of a preparation is defined relative to the amount of materialfrom the same organism. Thus, for example, a preparation of a particularpolypeptide that is 98% pure contains at most 2% of material from theorganism in which the polypeptide was produced.

In an even more preferred embodiment, the protein or polypeptide of theinvention contains less than 0.1%, preferably less than 10⁻²%, less than10⁻³%, less than 10⁻⁴%, less than 10⁻⁵% or even more preferably lessthan 10⁻⁶% of eukaryotic cellular material. In fact, since the inventionallows the production of high quantities of biologically active proteinsin bacteria, these proteins can be produced free of eukaryotic material.

Thus, the invention provides compositions, e.g., pharmaceuticalcompositions, comprising proteins produced according to the method ofthe invention. These compositions differ from previous preparations ofthe same type of protein in that, until now it has not been possible toproduce correctly folded complicated disulfide bond containing proteinsin high yields in prokaryotes, and thus, it has not previously beenpossible to obtain these proteins completely devoid of any eukaryoticcellular material. Thus, the proteins produced in prokaryotes accordingto the methods of the invention are particularly useful foradministration into humans, in view of the strict FDA requirements.

The polypeptides are preferably produced at an efficiency of at leastabout 1, 5, 10, 15, 20, 25, 30, 40, or more preferably at least about 50mg/l of host cell culture.

Preferred polypeptides or proteins which can be produced according tothe methods of the invention include any protein containing at least onedisulfide bond, or which, in the mature form does not contain adisulfide bond, but a precursor of which contained at least onedisulfide bond. Since most disulfide bond containing proteins aresecreted or membrane proteins, preferred proteins of the invention aresecreted or membrane proteins. The proteins can be eukaryotic,prokaryotic proteins, viral proteins, or plant proteins. Preferredproteins are of mammalian origin, and even more preferably of humanorigin. However, they can also be of murine, bovine, ovine, feline,porcine, canine, goat, equine, and primate origin.

Additional examples of proteins of interest which can be producedinclude the following proteins: mammalian polypeptides includingmolecules such as, e.g., renin, growth hormone, including human growthhormone; bovine growth hormone; growth hormone releasing factor;parathyroid hormone; thyroid stimulating hormone; lipoproteins; alpha1-antitrypsin; insulin A-chain; insulin B-chain; proinsulin;thrombopoietin; follicle stimulating hormone; calcitonin; luteinizinghormone; glucagon; clotting factors such as factor VIIIC, factor IX,tissue factor, and von Willebrands factor; anti-clotting factors such asProtein C; atrial naturietic factor; lung surfactant; a plasminogenactivator, such as urokinase or human urine or tissue-type plasminogenactivator (t-PA); bombesin; kallikreins; protease inhibitors; thrombin;hemopoietic growth factor; tumor necrosis factor-alpha and -beta;enkephalinase; a serum albumin such as human serum albumin;mullerian-inhibiting substance; relaxin A-chain; relaxin B-chain;prorelaxin; gonadotropin-associated peptide; a microbial protein, suchas beta-lactamase; Dnase; inhibin; activin; vascular endothelial growthfactor (VEGF); receptors for hormones or growth factors; integrin;protein A or D; rheumatoid factors; a neurotrophic factor such asbrain-derived neurotrophic factor (BDNF), neurotrophin-3, -4, -5, or -6(NT-3, NT-4, NT-5, or NT-6), or a nerve growth factor such as NGF-beta;cardiotrophins (cardiac hypertrophy factor) such as cardiotrophin-1(CT-1); platelet-derived growth factor (PDGF); fibroblast growth factorsuch as aFGF and bFGF; epidermal growth factor (EGF); transforminggrowth factor (TGF) such as TGF-alpha and TGF-beta, including TGF-beta1, TGF-beta 2, TGF-beta 3, TGF-beta 4, or TGF-beta 5; insulin-likegrowth factor-I and -II (IGF-I and IGF-II); des(1-3)-IGF-I (brainIGF-I), insulin-like growth factor binding proteins; CD proteins such asCD-3, CD-4, CD-8, and CD-19; erythropoietin; osteoinductive factors;immunotoxins; a bone morphogenetic protein (BMP); an interferon such asinterferon-alpha, -beta, and -gamma; colony stimulating factors (CSFs),e.g., M-CSF, GM-CSF, and G-CSF; interleukins (ILs), e.g., IL-1 to IL-10;anti-HER-2 antibody; superoxide dismutase; T-cell receptors; surfacemembrane proteins; decay accelerating factor; viral antigen such as, forexample, a portion of the AIDS envelope; transport proteins; homingreceptors; addressins; regulatory proteins; antibodies; and fragments ofany of the above-listed polypeptides.

The system is also particularly useful in the production of antibodies,such as single chain antibodies, as well as antibodies consisting ofmultiple polypeptide chains.

The polypeptides and proteins of the invention can be used for a greatvariety of purposes. Preferred uses include medical uses, includingdiagnostic uses, prophylactic and therapeutic uses. For example, theproteins can be prepared for topical or other type of administration.Another preferred medical use is for the preparation of vaccines.Accordingly, the proteins of the invention are solubilized or suspendedin pharmacologically acceptable solutions to form pharmaceuticalcompositions for administration to a subject. Appropriate buffers formedical purposes and methods of administration of the pharmaceuticalcompositions are further set forth below. It will be understood by aperson of skill in the art that medical compositions can also beadministered to subjects other than humans, such as for veterinarypurposes.

Examples of diagnostic uses include the use of a protein of theinvention as a binding agent, to detect specific proteins or DNA in acell sample or on a tissue section. Preferred proteins of the inventionfor this purpose include antibodies. Diagnostic methods using antibodiesor other binding agents are well known in the art and include flowcytometry, ELISA, and immunohistochemical methods.

Proteins of the invention can also be used for research purposes, e.g.,in research laboratories. In particular, at least some proteins of theinvention can be used as molecular weight markers.

Yet other proteins produced according to the method of the invention canbe used as nutritional sources or supplements. Such uses include withoutlimitation use as a protein or amino acid supplement, use as a carbonsource, use as a nitrogen source and use as a source of carbohydrate. Insuch cases the protein of the invention can be added to the feed of aparticular organism or can be administered as a separate solid or liquidpreparation, such as in the form of powder, pills, solutions,suspensions or capsules. In the case of microorganisms, the protein orpolynucleotide of the invention can be added to the medium in or onwhich the microorganism is cultured.

A protein of the invention be used in one or more of the followingpurposes or effects: inhibiting the growth, infection or function of, orkilling, infectious agents, including, without limitation, bacteria,viruses, fungi and other parasites; effecting (suppressing or enhancing)bodily characteristics, including, without limitation, height, weight,hair color, eye color, skin, fat to lean ratio or other tissuepigmentation, or organ or bodypart size or shape (such as, for example,breast augmentation or diminution, change in bone form or shape);effecting biorhythms or caricadic cycles or rhythms; effecting thefertility of male or female subjects; effecting the metabolism,catabolism, anabolism, processing, utilization, storage or eliminationof dietary fat, lipid, protein, carbohydrate, vitamins, minerals,cofactors or other nutritional factors or component(s); effectingbehavioral characteristics, including, without limitation, appetite,libido, stress, cognition (including cognitive disorders), depression(including depressive disorders) and violent behaviors; providinganalgesic effects or other pain reducing effects; promotingdifferentiation and growth of embryonic stem cells in lineages otherthan hematopoietic lineages; hormonal or endocrine activity; in the caseof enzymes, correcting deficiencies of the enzyme and treatingdeficiency-related diseases; treatment of hyperproliferative disorders(such as, for example, psoriasis); immunoglobulin-like activity (suchas, for example, the ability to bind antigens or complement); and theability to act as an antigen in vaccine composition to raise an immuneresponse against such protein or another material or entity which iscross-reactive with such protein.

Effective Dose and Administration of Therapeutic Compositions

Toxicity and therapeutic efficacy of compounds of the invention can bedetermined by standard pharmaceutical procedures in cell cultures orexperimental animals, e.g., for determining The Ld₅₀ (The Dose Lethal To50% Of The Population) And The Ed₅₀ (the dose therapeutically effectivein 50% of the population). The dose ratio between toxic and therapeuticeffects is the therapeutic index and it can be expressed as the ratioLD₅₀/ED₅₀. Compounds which exhibit large therapeutic induces arepreferred. While compounds that exhibit toxic side effects may be used,care should be taken to design a delivery system that targets suchcompounds to the site of affected tissue in order to minimize potentialdamage to uninfected cells and, thereby, reduce side effects.

The data obtained from the cell culture assays and animal studies can beused in formulating a range of dosage for use in humans. The dosage ofsuch compounds lies preferably within a range of circulatingconcentrations that include the ED₅₀ with little or no toxicity. Thedosage may vary within this range depending upon the dosage formemployed and the route of administration utilized. For any compound usedin the method of the invention, the therapeutically effective dose canbe estimated initially from cell culture assays. A dose may beformulated in animal models to achieve a circulating plasmaconcentration range that includes the IC₅₀ (i.e., the concentration ofthe test compound which achieves a half-maximal inhibition of symptoms)as determined in cell culture. Such information can be used to moreaccurately determine useful doses in humans. Levels in plasma may bemeasured, for example, by high performance liquid chromatography.

Pharmaceutical compositions for use in accordance with the presentinvention may be formulated in conventional manner using one or morephysiologically acceptable carriers or excipients. Thus, the compoundsand their physiologically acceptable salts and solvates may beformulated for administration by, for example, injection, inhalation orinsufflation (either through the mouth or the nose) or oral, buccal,parenteral or rectal administration.

For such therapy, the compounds of the invention can be formulated for avariety of loads of administration, including systemic and topical orlocalized administration. Techniques and formulations generally may befound in Remmington's Pharmaceutical Sciences, Meade Publishing Co.,Easton, Pa. For systemic administration, injection is preferred,including intramuscular, intravenous, intraperitoneal, and subcutaneous.For injection, the compounds of the invention can be formulated inliquid solutions, preferably in physiologically compatible buffers suchas Hank's solution or Ringer's solution. In addition, the compounds maybe formulated in solid form and redissolved or suspended immediatelyprior to use. Lyophilized forms are also included.

For oral administration, the pharmaceutical compositions may take theform of, for example, tablets or capsules prepared by conventional meanswith pharmaceutically acceptable excipients such as binding agents(e.g., pregelatinised maize starch, polyvinylpyrrolidone orhydroxypropyl methylcellulose); fillers (e.g., lactose, microcrystallinecellulose or calcium hydrogen phosphate); lubricants (e.g., magnesiumstearate, talc or silica); disintegrants (e.g., potato starch or sodiumstarch glycolate); or wetting agents (e.g., sodium lauryl sulphate). Thetablets may be coated by methods well known in the art. Liquidpreparations for oral administration may take the form of, for example,solutions, syrups or suspensions, or they may be presented as a dryproduct for constitution with water or other suitable vehicle beforeuse. Such liquid preparations may be prepared by conventional means withpharmaceutically acceptable additives such as suspending agents (e.g.,sorbitol syrup, cellulose derivatives or hydrogenated edible fats);emulsifying agents (e.g., lecithin or acacia); non-aqueous vehicles(e.g., ationd oil, oily esters, ethyl alcohol or fractionated vegetableoils); and preservatives (e.g., methyl or propyl-p-hydroxybenzoates orsorbic acid). The preparations may also contain buffer salts, flavoring,coloring and sweetening agents as appropriate.

Preparations for oral administration may be suitably formulated to givecontrolled release of the active compound. For buccal administration thecompositions may take the form of tablets or lozenges formulated inconventional manner. For administration by inhalation, the compounds foruse according to the present invention are conveniently delivered in theform of an aerosol spray presentation from pressurized packs or anebuliser, with the use of a suitable propellant, e.g.,dichlorodifluoromethane, trichlorofluoromethane,dichlorotetrafluoroethane, carbon dioxide or other suitable gas. In thecase of a pressurized aerosol the dosage unit may be determined byproviding a valve to deliver a metered amount. Capsules and cartridgesof e.g., gelatin for use in an inhaler or insufflator may be formulatedcontaining a powder mix of the compound and a suitable powder base suchas lactose or starch.

The compounds may be formulated for parenteral administration byinjection, e.g., by bolus injection or continuous infusion. Formulationsfor injection may be presented in unit dosage form, e.g., in ampoules orin multi-dose containers, with an added preservative. The compositionsmay take such forms as suspensions, solutions or emulsions in oily oraqueous vehicles, and may contain formulatory agents such as suspending,stabilizing and/or dispersing agents. Alternatively, the activeingredient may be in powder form for constitution with a suitablevehicle, e.g., sterile pyrogen-free water, before use.

The compounds may also be formulated in rectal compositions such assuppositories or retention enemas, e.g., containing conventionalsuppository bases such as cocoa butter or other glycerides.

In addition to the formulations described previously, the compounds mayalso be formulated as a depot preparation. Such long acting formulationsmay be administered by implantation (for example subcutaneously orintramuscularly) or by intramuscular injection. Thus, for example, thecompounds may be formulated with suitable polymeric or hydrophobicmaterials (for example as an emulsion in an acceptable oil) or ionexchange resins, or as sparingly soluble derivatives, for example, as asparingly soluble salt.

Systemic administration can also be by transmucosal or transdermalmeans. For transmucosal or transdermal administration, penetrantsappropriate to the barrier to be permeated are used in the formulation.Such penetrants are generally known in the art, and include, forexample, for transmucosal administration bile salts and fusidic acidderivatives. in addition, detergents may be used to facilitatepermeation. Transmucosal administration may be through nasal sprays orusing suppositories. For topical administration, the oligomers of theinvention are formulated into ointments, salves, gels, or creams asgenerally known in the art. A wash solution can be used locally to treatan injury or inflammation to accelerate healing.

The compositions may, if desired, be presented in a pack or dispenserdevice which may contain one or more unit dosage forms containing theactive ingredient. The pack may for example comprise metal or plasticfoil, such as a blister pack. The pack or dispenser device may beaccompanied by instructions for administration.

Kits of the Invention

For any of the above-described uses, including any or all of theseresearch utilities, the proteins can be commercialized as part of a kit,e.g., a kit of research products. Such a kit can comprise one or moreproteins produced according to the method of the invention, and anyadditional reagent, e.g., a buffer, a control reagent, and an antibodyagainst the protein.

In another embodiment, the kit comprises a host cell of the inventionand optionally an inducer, growth media, a plasmid encoding a protein ofinterest, a probe, an antibody, and/or instructions for use. Thus, a kitmay contain one or more necessary components for producing abiologically active or properly folded disulfide containing protein.Accordingly, a kit may comprise a host cell and instructions for use.Alternatively, a kit may comprise one or more reagents necessary for thepreparation of a host cell of the invention. Such a kit may compriseagent(s) for reducing the expression of reductases or agents necessaryfor introducing mutations into one or more reductases of a host cell. Akit may comprise agents necessary for improving the growth of hostcells, e.g., reducing agents, or a gene optionally contained in aplasmid, encoding a protein which improves growth, e.g., AhpC*.

The present invention is further illustrated by the following exampleswhich should not be construed as limiting in any way. The contents ofall cited references (including literature references, issued patents,published patent applications as cited throughout this application) arehereby expressly incorporated by reference.

The practice of the present invention will employ, unless otherwiseindicated, conventional techniques of cell biology, cell culture,molecular biology, transgenic biology, microbiology, recombinant DNA,and immunology, which are within the skill of the art. Such techniquesare explained fully in the literature. See, for example, MolecularCloning A Laboratory Manual, 2^(nd) Ed., ed. by Sambrook, Fritsch andManiatis (Cold Spring Harbor Laboratory Press: 1989); DNA Cloning,Volumes I and II (D. N. Glover ed., 1985); Oligonucleotide Synthesis (M.J. Gait ed., 1984); Mullis et al. U.S. Pat. No. 4,683,195; Nucleic AcidHybridization (B. D. Hames & S. J. Higgins eds. 1984); Transcription AndTranslation (B. D. Hames & S. J. Higgins eds. 1984); Culture Of AnimalCells (R. I. Freshney, Alan R. Liss, Inc., 1987); Immobilized Cells AndEnzymes (IRL Press, 1986); B. Perbal, A Practical Guide To MolecularCloning (1984); the treatise, Methods In Enzymology (Academic Press,Inc., N.Y.); Gene Transfer Vectors For Mammalian Cells (J. H. Miller andM. P. Calos eds., 1987, Cold Spring Harbor Laboratory); Methods InEnzymology, Vols. 154 and 155 (Wu et al. eds.), Immunochemical MethodsIn Cell And Molecular Biology (Mayer and Walker, eds., Academic Press,London, 1987); Handbook Of Experimental Immunology, Volumes I-IV (D. M.Weir and C. C. Blackwell, eds., 1986); Manipulating the Mouse Embryo,(Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1986).

EXAMPLES Example 1 Isolation of trxB gshA supp and trxB gor SuppressorStrains

This Example describes the isolation of suppressor mutants of the trxBgshA and trxB gor mutants, which grow at about the same rate as theirwild type parental strain E. coli DHB4.

For aerobic growth, E. coli depends on the presence of either of the twomajor thiol reduction systems—the thioredoxin and theglutathione-glutaredoxin pathways. When both of these pathways areeliminated by mutation, such as in a trxB gor or trxB gshA doublemutant, the cells grow extremely slowly (Prinz, et al. (1997) J. Biol.Chem. 272: 15661). These cells can, however, be rescued by the additionof the reductant DTT to the growth medium.

When grown in the presence of DTT, both the trxB gshA and trxB gorstrains give rise to fast growing derivatives at a high frequency. Sincethe trxB, gshA, and gor alleles in these strains are non-reverting nullmutations, the faster growing derivatives must result from extragenicsuppressor mutations.

Two fast growing suppressor mutants were obtained from the strains DHB4gshA20::Tn10 Km trxB::Km . . . Tn10 and DHB4 gor522 . . . mini-Tn10TctrxB::Km, both of which are derivatives of DHB4 (MC1000 phoA(PvuII) phoRmalF3 F′[lac+(lacIQ) pro]) (Boyd, et al. (1987) Proc Natl Acad Sci USA84: 8525), as follows. These fast growing suppressor mutants wereobtained by growing the two strains for about 24 hours in mediumcontaining 6 mM DTT. A fast growing strain from each of the two strainswere isolated: FA112 ((DHB4 gshA20::Tn10 Km trxB::Km . . . Tn10 supp)and FA113 (DHB4 gor522 . . . mini-Tn10Tc trxB::Km supp). Each of thesestrains was deposited at the ATCC on Nov. 11, 1999 under therequirements and terms of the Budapest Treaty, and have been assignedAccession Nos. PTA-938 (FA112) and PTA-939 (FA113), respectively.

For establishing the growth curve of the FA113 strain and compare it toits wild type parent strain, the bacteria were subjected to aerobicgrowth at 37° C. in LB medium in test tubes. The results, which arepresented in FIG. 3, show that at 37° C. in rich media, FA113 was foundto grow almost as well as the wild type (DHB4, trxB+ gor+) strain withdoubling times 30 and 27 minutes, respectively. In contrast, WP778, thetrxB gor parent of FA113 grew with a doubling time of 300 min in theabsence of DTT (Prinz, et al. (1997) J. Biol. Chem. 272: 15661).

Example 2 Proper Disulfide Bond Formation of MalS in the SuppressorStrains

This Example demonstrates the production of high amounts of thedisulfide bond containing protein MalS in the cytoplasm of a suppressormutant.

For determining whether any of the suppressed mutants still retains thehigh cytoplasmic oxidizing potential of the parental trxB gshA (FA112)or trxB gor (FA113) strains, the production of a variety of modelproteins was tested. Accordingly, a signal sequenceless version of MalS,a periplasmic amylase that contains 2 disulfide bonds, was expressed inFA112 and FA113. This construct is described Spiess et al. (1999) Cell97: 339. The amount and activity of the MalS enzyme produced by the twostrains was determined as described in Spiess et al. (1999) Cell 97:339. The results indicate that enzymatically active protein was detectedonly in the trxB gor supp strain FA113.

Example 3 Proper Disulfide Bond Formation of Multiple Disulfide BondContaining Proteins in the Suppressor Strains

This Example demonstrates that the following proteins which containmultiple disulfide bonds are produced at high levels and in a properconformation in the cytoplasm of a suppressor mutant: a version of mouseurokinase with six disulfide bonds only one of which is linear; atruncated form of the human tissue plasminogen activator (vtPA)consisting of the kringle 2 and protease domains with a total of ninedisulfide bonds (one linear); and the full-length human tPA containing17 disulfide bonds and one free cysteine.

The cytoplasmic expression of mouse urokinase devoid of signal sequence,full length human tPA, and human tPA devoid of signal sequence (aminoacids 6-175), all of which contain multiple disulfide bonds withnon-linear connectivities, was analyzed, and compared to the periplasmicexpression of these proteins. The amino acid sequence of human tPA isdescribed in Obukowicz, et al. (1990) Biochemistry 29: 9737. Forproduction of full length human tPA, the gene encoding full length humantPA was cloned into plasmid pTrc99A (trc promoter, Amp^(R), ColE1 ori;Amersham Pharmacia Biotech, Uppsala, Sweden) under the control of thetrc promoter, to yield plasmid pTrctPA. A vtPA gene encoding amino acids6-175 of human tPA was cloned into plasmid pTrc99A under the control ofthe trc promoter, to yield plasmid pTrcvtPA.

The amount of active urokinase was determined by zymography, asdescribed in Prinz et al. (1997) J. Biol. Chem. 272: 15661.

The amount of active vtPA and tPA was determined by fibrin clearanceassays as follows. Cells expressing either vtPA or full length tPA weregrown with shaking at 30° C. in LB medium supplemented with antibiotics(50 μg/ml Carbenicillin, 25 μg/ml Chloramphenicol) as needed. At OD6000.8, arabinose was added to 0.2% w/v final concentration; 30 minuteslater IPTG was added to 1 mM, and the culture was grown an additional 3hours. Cells were harvested by centrifugation, resuspended in cold PBS,and lysed in a French pressure cell. The insoluble fractions wereremoved by centrifugation (12,000×g, 10 min, 4° C.), and soluble proteinwas quantified by the Bio-Rad (Hercules, Calif.) protein assay, usingBSA as standard. Plasminogen activation was quantified by an indirectchromogenic assay as follows. In a microtiter plate, 5 μg of solubleprotein was added to wells containing 50 mM Tris-HCl pH 7.4, 0.01% Tween80, 0.04 mg/ml human glu-plasminogen (American Diagnostica, Greenwich,Conn.), and 0.4 mM Spectrozyme PL® (American Diagnostica); 260 μL finalvolume. The plate was then incubated at 37° C., and absorbance at 405 nmwas read after 2 or 3 hours. Activity is directly proportional to A405(i.e., absorbance at 405 nm), which is the absorbance after subtractingthe background of a strain lacking a vector expressing tPA. Relativeactivities were normalized to the A405 obtained by expressing vtPA alonein FA113.

In some experiments vtPA and tPA activities were determined bymonitoring fibrin clearance as previously described (Qiu, et al. (1998)Appl. Environ. Microbiol. 64: 4891; Waldenstrom, et al. (1991) Gene 99:243). Briefly, soluble protein (10 μg) from induced cultures was spottedonto fibrin/agarose plates and incubated for 24 hrs at 37° C. Clearancezones qualitatively measure biological activity of bacterially producedvtPA.

The results, which are shown in FIG. 3, indicated that for all threeproteins, substantially higher levels of active protein was detected inFA113 (trxB gor supp.), compared to the wild type, the trxB mutant, orthe trxB gshA supp strain FA112. A comparison of the fibrin clearancezones shown in FIG. 3 with a quantitative determination of the proteaseactivity of vtPA using a coupled assay that measures the activation ofplasminogen to plasmin revealed that the level of active vtPA in FA113is 10-fold higher than when expressed in the wild type strain DHB4, and2.5-fold higher than in the trxB gshA supp strain. Since the trxB gorsupp strain, FA113, gave the highest yields of active protein, it wasselected for more detailed characterization.

The growth rate of FA113/pTrcvtPA/pFA5 was compared to that of wild typeDHB4 and FA113. Expression of vtPA was induced at late log phase asdescribed above, and optical density was measured in a microtiter platereader. The results, which are shown in FIG. 4, indicate that bacterialgrowth of FA113 is not affected by the expression of a heterologouspolypeptide.

It was of interest to compare the formation of protein disulfides in thecytosol of the strain FA113 relative to a strain with the trxB gorphenotype that had not accumulated suppressor mutations. A directcomparison of the yields of disulfide-bonded proteins in FA113 and theparental strain WP778 is not meaningful because of the dramaticdifference in the growth rate of the two strains. Therefore, the strainFA222 in which the trxB gene was placed under the control of thearabinose promoter and which also contained the gor allele of FA113, wasconstructed as follows. Strain FA222 was derived from strain FA196,which was constructed as follows: a 1.0 kb fragment of DNA upstream oftrxB was first amplified by PCR, and a 441 bp fragment was generated bydigestion with NsiI. This 441 bp fragment was cloned into the NsiI siteof a pBAD33 vector (Guzman, et al. (1995) J. Bacteriol. 177: 4121) withtrxB cloned under the control of the arabinose promoter. The completeconstruct containing the 441 bp upstream region, the araC repressor geneand the arabinose controlled trxB allele was subcloned into the vectorpK0V (obtained from G. Church, Harvard Medical School) followed byintegration into the chromosome of E. coli DHB4 using the publishedprocedure of Link et al. (Link, et al. (1997) J. Bacteriol. 179: 6228),generating FA196. P1 transduction of the gor522 . . . mini-Tn10 allele(Prinz, et al. (1997) J. Biol. Chem. 272: 15661) to FA196 resulted instrain FA222.

The FA222 strain grows well in the presence of arabinose but exhibits atrxB gor phenotype when transferred to growth media lacking arabinose.Under these conditions, the accumulation of mouse urokinase in thecytosol of FA222 was comparable to that obtained in FA113. Thus, whilethe suppressor mutation alleviates the growth defect of trxB gor, itdoes not interfere with disulfide bond formation in the cytoplasm.

Example 4 Proper and Efficient Disulfide Bond Formation of OxyR in FA113

Exposure of E. coli to elevated concentrations of hydrogen peroxide ordiamide renders the cytoplasm more oxidizing and, among other things,results in the formation of a disulfide bond in the transcription factorOxyR. The oxidized form of OxyR activates the transcription of trxCencoding thioredoxin 2 and several other genes that play a role inprotecting the cell from oxidative damage (Zander, et al. (1998) MethodsEnzymol. 290: 59) (Ritz, et al. (2000) J. Biol. Chem. 275: 2505). FA113exhibited nearly full activation of OxyR as judged by the expression ofTrxC and the level of oxyS RNA. Thus, proper disulfide bonds are formedin OxyR in FA113.

Example 5 Oxidized Alkaline Phosphatase Accumulates in the Cytoplasm ofFA113 Cells

Pulse-chase experiments were carried out to determine the rate ofprotein oxidation in signal sequenceless alkaline phosphatase. E. colialkaline phosphatase contains 2 disulfide bonds linking cysteines thatare consecutive in the primary sequence, a property referred to aslinear cysteine connectivity.

E. coli DHB4 expressing alkaline phosphatase devoid of signal sequence(plasmid pAID135) was constructed as follows (Derman et al. (1993) EMBOJ. 12:879). Cells were diluted 1:100 from overnight cultures into M63supplemented with all 18 amino acids except methionine and cysteine andgrown at 37° C. When the cells reached an OD₆₀₀ of 0.2, IPTG was addedto 2 mM to induce expression of alkaline phosphatase. The pulse chasewas started by the addition of [³⁵S]methionine. After one minute,unlabeled methionine at 0.1% w/v (final concentration) was added andsubsequently, samples were collected at the indicated time points (seeFIG. 5) and mixed with 0.1 M iodoacetamide. The alkaline phosphatase wasthen immunoprecipitated and separated by native PAGE, such that theoxidized form (ox) was distinguished from the reduced form (red). OmpAwas used as an internal standard.

The results, which are presented in FIG. 5, show that, in FA113, about50% of the alkaline phosphatase was oxidized within one minute and wasmore than 95% complete after 11 minutes. The kinetics of disulfide bondformation in the trxB gor supp strain were slightly faster than in atrxB mutant. In contrast, no oxidized alkaline phosphatase accumulatedin the wild type strain even after 11 minutes.

Thus, properly formed and oxidized alkaline phosphatase forms in thecytoplasm of the TrxB gor supp mutant FA113.

Example 6 Coexpression of a Variant of a Thioredoxin VariantSignificantly Improves Disulfide Bond Formation

Stewart et al. (Stewart, et al. (1998) EMBO J. 17: 5543) have shown thatdisruption of trxB results in an accumulation of oxidized thioredoxinswhich can then act as oxidases, the reverse of their normal role.Likewise, in FA113, TrxA expressed from the chromosome was presentsolely in the oxidized form. We examined the effect of high levelexpression of TrxA and TrxA mutant proteins with varying redoxpotentials on the folding of the more complex multi-disulfide proteins,namely vtPA and tPA. The redox potential of most cysteineoxidoreductases, including TrxA, is strongly influenced by the sequenceof the dipeptide within the CXXC (SEQ ID NO: 1) active site motif(Mossner, et al. (1999) J. Biol. Chem. 274: 25254; Mossner, et al.(1998) Protein Sci. 7: 1233; Grauschopf, et al. (1995) Cell 83: 947).TrxA with a wild type active site (-CGPC-; SEQ ID NO: 2) and fivemutants with varying redox potentials (see below) were cloned intoplasmid pBAD33 (Gunzman et al. (1995) J. Bacteriol. 177:4121) under thecontrol of the araBAD promoter and transformed into FA113 together witha compatible expression vector for vtPA or full length tPA synthesis.

The active site mutants of wild type TrxA that were used were asfollows: -CGSC- (SEQ ID NO: 3); -CPYC- (SEQ ID NO: 4), which is theactive site found in wild type Grx proteins; --CPHC- (SEQ ID NO: 5),which is the active site found in the wild type DsbA protein; -CGHC-(SEQ ID NO: 6), which is the active site found in the wild type ratprotein disulfide isomerase (PDI); and -CGPA- (SEQ ID NO: 7).

Thioredoxin 1 (TrxA) and active-site mutants were amplified from theconstructs of Huber et al. (1986) J. Biol. Chem. 261: 15006, and Mossneret al. (1999) J. Biol. Chem. 274: 25254 and Mossner et al. (1998)Protein Sci. 7:1233. Rat PDI was amplified from a construct of De Sutteret al. (1994) Gene 141:163.

The transformed cells were then induced with arabinose followed byaddition of IPTG 30 minutes later to initiate synthesis of the tPAprotein, and the yield of active tPA was analyzed three hours later byan indirect assay for plasminogen activation employing a chromogenicplasmin substrate (see Example 3). Activity has been normalized to thevalue obtained from vtPA expressed alone in FA113.

Western blot analysis was undertaken as a control for the amount of TrxAprotein and variants expressed in each strain. Anti-TrxA antibodies werepurchased from Sigma (St. Louis, Mo.). The blots indicated that TrxA andthe TrxA variants accumulated to the same level at steady state.

The in vivo redox states of TrxA and the “Grx-like” TrxA variant wereassayed by derivatization of free thiols by4-acetamido-4′-maleimidyl-stilbene-2,2′-disulfonic acid (MolecularProbes, Eugene, Oreg.) and western blotting as described previously(Joly, et al. (1997) Biochemistry 36: 10067).

The results, which are shown in FIG. 6, indicate that overexpression ofTrxA resulted in a modest increase in the level of active vtPA. However,co-expression of more oxidizing TrxA variants gave significantly higheraccumulation of active vtPA. For example, co-expression of a moreoxidizing variant with the active site of GrxA (glutaredoxin 1) resultedin active vtPA at levels 15-fold greater than the control.

Analysis of the in vivo redox state of overexpressed TrxA revealed thatthe wild-type enzyme is present primarily in the oxidized form, with aminor fraction in the reduced state. In contrast, the mutant with the“Grx-like” active site is mainly reduced. GrxA (glutaredoxin 1)co-expression was much less effective than the “Grx-like” TrxA,presumably a consequence of its lower redox potential and the fact thatglutaredoxin is a less efficient catalyst of disulfide bond formation orreduction compared to thioredoxin (Aslund, et al. (1997) J. Biol. Chem.272: 30780). Similar relative increases to those reported above wereobtained with the full length tPA substrate. Interestingly,co-expression of the “Grx-like” TrxA variant significantly improveddisulfide bond formation not only in FA113 but also in the trxB gshAsupp strain FA112 and in the trxB mutant WP597 (DHV4 trxB::Km) asdetermined by fibrin clearance assays, as described in Example 3 (FIG.3).

Thus, the results of this Example show that cotransformation of TrxB gorsupp mutant with a plasmid encoding a thioredoxin variant having ahigher redox potential than its wild type coutnerpart significantlyincreases the production of proteins containing multiple disulfide bondsin the cytoplasm of these cells.

Example 7 Coexpression of a Disulfide Bond Isomerase Greatly IncreasesProduction of Proteins with Multiple Disulfide Bonds

This Example shows that causing DsbC to be localized to the cytoplasmenhances the yield of properly assembled disulfide-containing proteinsand compares the accumulation of properly formed tPA in the periplasmand cytoplasm of wild type and trxB gor supp mutants co-transformed withan additional catalyst of disulfide bond isomerization.

The folding of proteins containing multiple disulfide bonds withnon-linear connectivities is greatly assisted by the addition ofcatalysts that enhance the rate of disulfide bond isomerization. In theE. coli periplasm, the formation of active urokinase and tPA iscritically dependent on the DsbC disulfide isomerase activity (Qiu, etal., (1998) Appl. Environ. Microbiol. 64: 4891; Rietsch, et al. (1997)J. Bacteriol. 179: 6602). A version of DsbC without a signal sequence(amino acids 2-20) was constructed and placed behind the araBAD promoterin plasmid pBAD33 (araBAD promoter, Cm^(R), pACYC ori; Guzman et al.(1995) J. Bacteriol. 177:4121) and an optimized ribosome binding site toachieve efficient translation, to yield plasmid pBADSSdsbC. A version ofDsbA without a signal sequence (amino acids 2-19) was constructed andplaced behind the araBAD promoter in plasmid pBAD33 and an optimizedribosome binding site, to yield plasmid pBADSSdsbA. Anti-DsbC antibodieswere from John Joly (Genentech, South San Francisco, Calif.).

DsbC overexpressed in the cytoplasm of FA113 was found predominantly ina form where its structural disulfide had formed, but the active sitewas reduced. A 20-fold increase in vtPA activity was observed,corresponding to the highest accumulation of active protein in thisstudy (FIG. 7). In contrast, co-expression of DsbA under identicalconditions actually reduced the accumulation of active vtPA. The effectof the eukaryotic rat PDI (plasmid pBADrPDI consisting of mature rat PDIin pBAD33 with optimized RBS) expressed in the cytoplasm was alsoevaluated, but the increase in vtPA activity compared to the controlcells without any foldase overexpression was marginal.

It is instructive to compare the formation of protein disulfide bondsfollowing secretion in the periplasm of a wild type strain or in thecytoplasm of FA113. For this purpose, the vtPA gene was fused to abacterial signal peptide from the heat stable enterotoxin II. Forperiplasmic expression, vtPA as well as the full length tPA weretargeted for secretion by fusion to the heat-stable enterotoxin IIsignal sequence, referred to as “StII leader” (see, Qiu, et al. (1998)Appl. Environ. Microbiol. 64: 4891), to yield plasmids pTrcStIIvtPA andpTrcStIItPA, respectively. Transformation of each of these plasmids intothe bacterial strains and selection of positive clones was performed asdescribed above.

Secretion of vtPA in the periplasm of FA113 resulted in a lower yield ofactive protein relative to DHB4. However, when vtPA was expressed in thecytoplasm of FA113 a higher level of active protein was obtainedcompared to that obtained in the periplasm of the wild type counterpart,DHB4 (FIG. 7, columns 1 and 4). Analysis by Western blotting revealedthat the total level of tPA accumulation at steady state wasapproximately the same in the cytoplasm of FA113 and in the periplasm ofDHB4. The amount of active vtPA in the periplasm of DHB4 could beincreased by more than two orders of magnitude by co-expression ofperiplasmic DsbC. Co-expression of a signal sequenceless DsbC with vtPAin the cytoplasm of the trxB gor supp strain resulted in even higheraccumulation of correctly folded protein. Under these conditions thelevel of active vtPA represented a 2-fold increase relative toperiplasmic expression and a 200-fold increase compared to expression inthe cytoplasm of DHB4. Moreover, whereas high level expression of DsbCand vtPA in the periplasm resulted in growth arrest, cytoplasmicexpression did not have any appreciable effect on cell growth.

Thus, these new strains grow normally, even though the cytoplasm ishighly oxidizing, and favor the formation of disulfide bonds in certainproteins with an efficiency even higher than that of the periplasm. Forall the model eukaryotic proteins including the highly complex fulllength tPA, expression in the cytoplasm of the new strains resulted inappreciable yields of active protein exceeding that which could beobtained by periplasmic expression.

Example 8 The Suppressor Mutation in FA113 is Localized in the AlkylHydroperoxidase Subunit ahpC

This example describes the identification of the suppressor mutation inFA113, i.e., the mutation allowing this E. coli strain to grow similarlyto the wild type E. coli, by genetic mapping techniques, DNA sequencingand a series of strain constructions, essentially as described inincluding the technique described in Kleckner et al. (1991) Meth. Enzym.204:139. The suppressor mutation was mapped to a region near the ahpC,Fgene cluster, using linkage to a transposon insertion in the chromosome.These studies show that the mutation alters the gene ahpC which encodesthe peroxidase subunit of alkyl hydroperoxidase.

A transposon, called Tn10, carrying chloramphenicol resistance, wasallowed to insert randomly around the bacterial chromosome of the strainFA113. This was made possible by infecting the cell with a lambda phage,λNK1324, carrying the transposon which is able to transpose from thephage genome to the bacterial genome. This procedure yielded acollection of derivatives of FA113, each of which had a transposon at adifferent position in the bacterial chromosome. A large collection ofthese derivatives was pooled, grown up and infected with the P1 phage, aphage that is able to transduce small pieces of chromosomal DNA from onestrain to another.

It is expected that among the strains with transposon insertions inthem, approximately 1% would have a transposon close enough to thesuppressor locus that a piece of DNA could be incorporated into a P1transducing phage carrying both a transposon and the suppressormutation. These would be strains in which the transposon was “tightlylinked” to the suppressor mutation. This P1 lysate was used to transducea recipient E. coli strain that was trxB⁻, gor⁻ and carried a plasmidthat carries a wild-type trxB gene (strain referred to as JL10), thusallowing these strains to grow in the absence of a suppressor. Since thewild-type trxB gene was under the control of thearabinose-inducible/glucose-repressible araBAD promoter, this strainexpressed the wild type trxB gene when grown in the presence ofarabinose, and repressed the expression of the gene in the presence ofglucose.

Chloramphenicol-resistant transductants of this E. coli strain wereobtained and screened for those that were no longer dependent on thetrxB plasmid for growth. These should have the suppressor mutation inthem such that the trxB, gor, supp strain can grow. The conversion toindependence of this plasmid could be demonstrated by shutting off theexpression of the trxB gene on the plasmid that itself was dependent onarabinose for its expression (i.e., culture in the absence of arabinoseand in the presence of glucose) and subsequent loss of the plasmidresistance.

These candidates for strains in which the transposon is close to thesuppressor gene were verified by making new P1 lysates on these strainsand showing that these lysates could now transduce together thechloramphenicol resistance and the suppressor phenotype at highfrequency. Several colonies that conferred Cm-resistance and suppressedthe growth defect were obtained.

The position on the chromosome where these transposons had inserted wasdetermined by using arbitrary polymerase chain reaction to amplifysequences that run from the transposon into the neighboring portion ofthe chromosome, as described in Ritz, et al. (2000) J. Biol. Chem. 275:2505 and in O'Toole, G. A., Kolter, R. (1998) Mol. Microbiol.28:449-461. The sequence of the chromosomal region determined in thisway indicated exactly where the transposon has inserted in thechromosome since the entire sequence of the E. coli genome is known.This analysis indicated that all of the insertions mapped betweenminutes 13 and 14, i.e., a region close to the ahpC,F locus.

Sequence analysis of the entire locus, i.e., the ahpC and ahpF genes,from a wild type and 10 different suppressor strains revealed thepresence of a mutation in the ahpC gene. This mutation lies in a repeatsequence of 4 TCT triplets in the gene (see FIG. 8A). The mutationamplifies this sequence with an additional repeat of the triplet,resulting in the insertion of a phenylalanine (codon 38) 9 amino acidsfrom the active site cysteine (codon C47) of AhpC. This mutant isreferred to as ahpC*.

FIG. 8B shows that the region of the protein that contains the mutationis highly conserved in homologous proteins in other microorganisms andin the corresponding human gene (TSA).

Example 9 AhpC* Restores Normal Growth to a trxB gor Double Mutant

This example demonstrates that the mutational change in AhpC wasnecessary and sufficient to suppress the growth defect of the doublemutant JL10.

The open reading fromes coding for ahpCF were amplified from thechromosome of the wild type and the FA113 mutant by PCR and cloned intothe pACYC derivative pLAC-YC. Constructs containing either the entireoperon or just the ahpC-gene (wild type or mutant) were transformed intoJL10 and DR456, in which in addition to the trxB and gor mutations, theahpCF locus is also inactivated. DR456 is also referred to as “trxB gorahpCF::Km mutant”. Growth of each of these strains was determined onrich medium (NZ).

The results, which are shown in Table 2, indicate that AhpC* is requiredto restore normal growth in a trxB gor strain (having an inactivatingmutation in trxB and gor), thus indicating that the mutation identifiedin Example 8 is indeed responsible for the restoration of the ability ofthis strain to grow similarly to a corresponding wild type strain. Inaddition, since the trxB gor mutants have a wild type AhpC gene, thesuppressor mutation in AhpC* is dominant.

TABLE 2 Ability of strains to grow on NZ Relevant genotype Gene(s)introduced Growth on NZ trxB gor No trxB gor ahpCF::Km No trxB gorpLAC-ahpCF No trxB gor pLAC-ahpC No trxB gor pLAC-ahpF No trxB gorpLAC-ahpC*F Yes trxB gor pLAC-ahpC* Yes trxB gor ahpCF::Km pLAC-ahpC NotrxB gor ahpCF::Km pLAC-ahpF No trxB gor ahpCF::Km pLAC-ahpC*F Yes trxBgor ahpCF::Km pLAC-ahpC* No

The results also indicate that AhpF is required for the suppressoreffect of the mutation in AhpC*, since introduction of pLAC-ahpC* alonein the strain that is deficient in AhpC and AhpF (trxB gor ahpCF:Km)does not allow growth of the strain in NZ. Thus, both AhpC* and AhpF arerequired to suppress DR456.

Thus, the results of this example proved that the addition of a singleamino acid to AhpC abolishes the severe growth defect of strains such asFA113. In addition, the results indicated that the effect of AhpC* isdominant over the wild-type allele.

Example 10 AhPC* has Lost its Peroxidase Activity

This example demonstrates that the mutation in AhpC* eliminatesessentially all of its peroxidase activity.

To determine whether AhpC* retained its original peroxidase function,e.g., its ability, together with AhpF, to confer increased resistance toalkyl peroxides in vivo, the following test was performed. Each of theoperons AhpCF and AhpC*F were introduced into the high copy numberplasmid pBAD18 Km under the control of the araBAD promoter andintroduced into wild type E. coli. As expected, the E. coli straincontaining the plasmid with the AhpCF operon exhibited increasedresistance to cumene hydroperoxide (CuHP) relative to E. coli thatcontained a control plasmid that does not contain an AhpCF operon (seeTable 3). As indicated in the table, after a 10 min exposure to 5 μMCuHP, a 10-times greater fraction of cells survived (3.2%) as comparedto a vector-only control (pLAC-YC) (0.3%). The mutant AhpC* (pLAC-C*F)on the other hand did not exhibit any significant peroxidase activity asthe fraction of surviving cells was the same as in the control (0.3%).Both, AhpC and AhpC* were expressed at similarly high levels, asindicated by Coomassie stained gels.

TABLE 3 Percentage of E. coli cells alive after incubation in CuHPRelevant genotype plasmid introduced CuHP survival (%) Wt pLAC-YC 0.3 WtpLAC-ahpCF 3.2 Wt pLAC-C*F 0.3

Thus, expression of AphC* reduces essentially all of the ability of awild type E. coli strain to survive in oxidizing condition.

The OxyR-dependent stress response in strains containing either ahpC orahpC* was also determined. This was undertaken by introducing intovarious E. coli strains described above a plasmid including atrxC′-′lacZ fusion gene, in which the LacZ gene is under the control ofthe trxC promoter. The absence of a functional AhpCF-peroxidase systemis known to increase the expression of such a construct (Ritz et al.(2000) J. Biol. Chem. 275:2505), probably because the intracellularperoxide levels are elevated in those circumstances, resulting in bindigof OxyR to the trxC promoter and activation of transcription of the lacZgene.

TABLE 4 Expression level of beta-galactosidase in various E. colistrains Relevant genotype beta-Galactosidase activity Wt 61 AhpCF::Km393 AhpCF..Tn10Cm 79 AhpC*F..Tn10Cm 409

As shown in Table 4, it was found that strains expressing AhpC* (ahpC*F. . . Tn10Cm) had similar expression levels of beta-galactosidase tothose obtain with a strain that does not have a functional AhpCF system(ahpCF::Km). These results further confirm that AhpC* has lost theability to function as an alkyl hydroperoxidase in vivo.

Example 11 AhpC* Cannot Restore Normal Growth Without Glutathione orGlutaredoxin 1

This example demonstrates that restoration of wild type growth of a trxBgor mutant requires the activity of at least some reductases of theglutaredoxin system, but not of the thioredoxin system.

As described in the above Examples, disulfide bonds can efficiently beintroduced into model proteins, such as urokinase and human tissuepasminogen activator, in trxB gor suppressor strains, even when thesemodel proteins are expressed only in the cytoplasm of E. coli. Yet, thestrains must retain some disulfide reducing capacities as electrons mustbe transferred to essential reductive enzymes such as ribonucleotidereductase or PAPS reductase (the latter only for growth on minimalmedia). To determine which reductases may be necessary in AhpC*containing strains, additional mutations were introduced into genes ofthe trxB gor AhpC* (JL19.2) strain, and tested these mutants for theirability to grow on rich medium in the presence of glucose (i.e., inconditions under which the expression of trxB is suppressed).

The results, which are presented in Table 5, indicate that bothfunctional glutathione and glutaredoxin 1 are necessary to permit trxBgor ahpC* mutants to grow on rich medium, wherease none of thecomponents of the thioredoxin branch (trxA and trxC) were required.These results indicate that AhpC* probably functions as a thiolreductase to replace at least partially glutathione oxido reductase inthe double mutant.

TABLE 5 Ability of strains to grow on NZ Relevant genotype Growth onrich medium TrxB gor No TrxB gor ahpC* Yes TrxB gor ahpC* gshA Yes TrxBgor ahpC* grxA Yes TrxB gor ahpC* trxA trxC Yes

Example 12 Assay to Determine Whether AhpC* has Glutathione(Glutaredoxin) Activity

Alkyl hydroperoxidase, product of the ahpC and ahpF genes, is areductant that passes electrons along pairs of cysteines much as otherproteins in thioredoxin and glutaredoxin pathways do (see FIGS. 9 and10). Thus, it is not surprising that this protein might be altered tocompensate for some of the defective reducing activity of the trxB,gormutant. As described in Example 10, examination of the response of thesuppressor strains to hydrogen peroxide showed that the suppressormutation reduces the peroxidase activity of this protein. At the sametime, AphC* appears to have gained a new activity, since in a straincarrying both the suppressor mutation and a wild-type copy of the ahpC,the suppressor mutation is dominant (see Examples 9 and 10). Byintroducing the suppressor into strains carrying an additional defect inglutaredoxin 1 expression (grxA⁻) or in glutathione biosynthesis (gshA),it was shown that the effectiveness of the suppressor is dependent onthe glutathione-glutaredoxin pathway. It is thus likely the suppressormutation restores the growth capabilities of trxB gor mutants, byaltering AhpC so that it can reduce oxidized glutaredoxin 1 eitherdirectly or by reducing glutathione (see FIG. 11). Thus, the mutantenzyme restored reducing capacity to the cytoplasm sufficient to allowgrowth.

To determine whether AhpC* has reducing activity, in particular, that itcan transfer electrons fom NADH to glutaredoxin 1 directly or viaglutathione, several assays could be used. For example, one can produceand purify AhpC and AhpC* and use each of these purified proteinstogether with the reductase AhpF in a glutathione reductase assay. Aglutathione reductase assay is well known in the art.

EQUIVALENTS

Those skilled in the art will recognize, or be able to ascertain usingno more than routine experimentation, many equivalents of the specificembodiments of the invention described herein. Such equivalents areintended to be encompassed by the following claims.

1. A prokaryotic cell that is genetically modified to shift the redox status of the cytoplasm to a more oxidative state, which cell further expresses a heterologous polypeptide selected from the group consisting of catalysts of disulfide bond formation, disulfide bond isomerization and the combination of disulfide bond formation and disulfide bond isomerization, and which cell is further modified to increase its ability to proliferate, wherein the modification to increase its ability to proliferate is a mutation in an AhpC gene.
 2. The prokaryotic cell of claim 1, wherein the expression or activity of a reductase is decreased relative to that in the corresponding wild type cell.
 3. The prokaryotic cell of claim 2, wherein the reductase is selected from the group consisting of thioredoxin reductase, glutathione reductase, and glutathione.
 4. The prokaryotic cell of claim 3, in which the expression or activity of a second reductase is decreased relative to that in the corresponding wild type cell.
 5. The prokaryotic cell of claim 4, wherein the second reductase is selected from the group consisting of thioredoxin reductase, glutathione reductase, and glutathione.
 6. The prokaryotic cell of claim 2, wherein the gene encoding the reductase is mutated.
 7. The prokaryotic cell of claim 6, wherein the gene encoding the reductase contains a null mutation.
 8. The prokaryotic cell of claim 5, wherein the genes encoding the first and the second reductases contain a null mutation.
 9. The prokaryotic cell of claim 2, wherein the activity of the reductase is inhibited.
 10. The prokaryotic cell of claim 9, wherein the activity of the reductase is inhibited by contacting the prokaryotic cell with an agent.
 11. The prokaryotic cell of claim 1, wherein the modification to increase the ability of the cell to proliferate is a mutation in the endogenous ahpC gene.
 12. The prokaryotic cell of claim 1, wherein the mutation is located in a region containing four triplet repeats.
 13. The prokaryotic cell of claim 12, wherein the mutated ahpC protein comprises the amino acid sequence set forth in SEQ ID NO:
 24. 14. The prokaryotic cell of claim 12, wherein the mutation in the ahpC gene comprises an insertion of three nucleotides in the TCT triplet repeat region located at about codons 36-39 of an ahpC gene.
 15. The prokaryotic cell of claim 14, wherein the triplet rich region of the mutated ahpC gene encodes a stretch of four phenylalanines.
 16. The prokaryotic cell of claim 14, wherein the three nucleotides are TCT.
 17. The prokaryotic cell of claim 15, wherein the mutated ahpC gene encodes a protein comprising SEQ ID NO:
 11. 18. The prokaryotic cell of claim 17, wherein the TCT triplet rich region has the nucleotide sequence set forth in SEQ ID NO:
 10. 19. The prokaryotic cell of claim 1, which is a prokaryotic cell having ATCC Designation No. PTA-938 (FA112) and further expresses a heterologous polypeptide selected from the group consisting of catalysts of disulfide bond formation, disulfide bond isomerization and the combination of disulfide bond formation and disulfide bond isomerization.
 20. The prokaryotic cell of claim 1, which is a prokaryotic cell having ATCC Designation No. PTA-939 (FA113) and further expresses a heterologous polypeptide selected from the group consisting of catalysts of disulfide bond formation, disulfide bond isomerization and the combination of disulfide bond formation and disulfide bond isomerization.
 21. A prokaryotic cell of claim 1, further comprising a heterologous nucleic acid encoding a protein comprising at least one cysteine that forms a disulfide bond with another cysteine.
 22. The prokaryotic cell of claim 1, wherein the heterologous polypeptide is a catalyst of disulfide bond isomerization.
 23. The prokaryotic cell of claim 22, wherein the reductase is selected from the group consisting of thioredoxin reductase, glutathione reductase, and glutathione.
 24. The prokaryotic cell of claim 23, in which the expression or activity of a second reductase is decreased relative to that in the corresponding wild type cell.
 25. The prokaryotic cell of claim 24, wherein the second reductase is selected from the group consisting of thioredoxin reductase, glutathione reductase, and glutathione.
 26. The prokaryotic cell of claim 23, wherein the gene encoding the reductase is mutated.
 27. The prokaryotic cell of claim 26, wherein the gene encoding the reductase contains a null mutation.
 28. The prokaryotic cell of claim 24, wherein the genes encoding the first and the second reductases contain a null mutation.
 29. The prokaryotic cell of claim 22, wherein the modification to increase the ability of the cell to proliferate is a mutation in the endogenous ahpC gene.
 30. The prokaryotic cell of claim 29, wherein the mutation in the ahpC gene comprises an insertion of three nucleotides in the TCT triplet repeat region located at about codons 36-39 of an ahpC gene.
 31. The prokaryotic cell of claim 30, wherein the three nucleotides are TCT.
 32. The prokaryotic cell of claim 31, wherein the mutated ahpC protein comprises the amino acid sequence set forth in SEQ ID NO:
 24. 33. A prokaryotic cell of claim 22, further comprising a heterologous nucleic acid encoding a protein comprising at least one cysteine that forms a disulfide bond with another cysteine.
 34. A method for producing a protein having at least one cysteine, which forms a disulfide bond with another cysteine, comprising isolating the protein from a cell of claim 22 in which has been introduced a nucleic acid encoding the protein, which protein has at least one cysteine that forms a disulfide bond with another cysteine, and which cell has been grown under conditions in which the protein is produced.
 35. The prokaryotic cell of claim 1, wherein the catalyst is a DsbC protein without a signal sequence or a variant thereof that is encoded by a nucleic acid that hybridizes to a nucleic acid encoding a DsbC protein under conditions including a wash in 0.2×SSC at 50° C., wherein the variant acts as a catalyst selected from the group consisting of catalysts of disulfide bond formation, disulfide bond isomerization and the combination of disulfide bond formation and disulfide bond isomerization.
 36. The prokaryotic cell of claim 1, wherein the catalyst is a variant of a protein of the thioredoxin superfamily having a redox potential that is higher than that of its wild type counterpart.
 37. The prokaryotic cell of claim 36, wherein the variant is a “Grx” variant of thioredoxin A.
 38. The prokaryotic cell of claim 35, wherein the catalyst is a DsbC protein without a signal sequence.
 39. A method for producing a protein having at least one cysteine, which forms a disulfide bond with another cysteine, comprising isolating the protein from a cell of claim 1 in which has been introduced a nucleic acid encoding the protein, which protein has at least one cysteine that forms a disulfide bond with another cysteine, and which cell has been grown under conditions in which the protein is produced. 